FF12878
FFPE from B-Lymphocyte
Description:
CEPH/UTAH PEDIGREE 1463
INTERNATIONAL HAPMAP PROJECT - CEPH (PLATE I) [UTAH RESIDENTS WITH ANCESTRY FROM NORTHERN AND WESTERN EUROPE]
CYTOCHROME P450, SUBFAMILY IIC, POLYPEPTIDE 19; CYP2C19
INTERNATIONAL HAPMAP PROJECT - CEPH [UTAH RESIDENTS WITH ANCESTRY FROM NORTHERN AND WESTERN EUROPE]
NA CUSTOM SERVICE PLATE 01
|
Repository
|
NIGMS Human Genetic Cell Repository
|
| Subcollection |
CEPH
Repository Linkage Families
Pharmacogenetics
PIGI Consented Sample |
|
Biopsy Source
|
Peripheral vein
|
|
Cell Type
|
B-Lymphocyte
|
|
Tissue Type
|
Blood
|
|
Transformant
|
Epstein-Barr Virus
|
|
Sample Source
|
FFPE from B-Lymphocyte
|
|
Race
|
White
|
|
Ethnicity
|
UTAH/MORMON
|
|
Country of Origin
|
USA
|
|
Family Member
|
2
|
|
Relation to Proband
|
mother
|
|
Confirmation
|
Clinical summary/Case history
|
|
Species
|
Homo sapiens
|
|
Common Name
|
Human
|
|
Remarks
|
|
| IDENTIFICATION OF SPECIES OF ORIGIN |
Species of Origin Confirmed by Nucleoside Phosphorylase, Glucose-6-Phosphate Dehydrogenase, and Lactate Dehydrogenase Isoenzyme Electrophoresis |
| |
| IDENTIFICATION OF SPECIES OF ORIGIN |
Species of Origin Confirmed by Nucleoside Phosphorylase, Glucose-6-Phosphate Dehydrogenase, and Lactate Dehydrogenase Isoenzyme Electrophoresis |
| |
| Remarks |
Mother; donor subject has a single bp (G-to-A) transition at nucleotide 681 in exon 5 of the CYP2C19 gene (CYP2C19*2) which creates an aberrant splice site. The change altered the reading frame of the mRNA starting with amino acid 215 and produced a premature stop codon 20 amino acids downstream, resulting in a truncated, nonfunctional protein. Because of the aberrant splice site, a 40-bp deletion occurred at the beginning of exon 5 (from bp 643 to bp 682), resulting in deletion of amino acids 215 to 227. The truncated protein had 234 amino acids and would be catalytically inactive because it lacked the heme-binding region. |
| Quail MA, Corton C, Uphill J, Keane J, Gu Y, Identifying the best PCR enzyme for library amplification in NGS Microbial genomics10: 2024 |
| PubMed ID: 38578268 |
| |
| Xu B, Gao X, Li X, Li F, Zhang Z, Crosslinking intensity modulates the reliability and sensitivity of chromatin conformation detection at different structural levels Communications biology7:1216 2024 |
| PubMed ID: 39349577 |
| |
| Zubiaur P, Rodríguez-Antona C, Boone EC, Daly AK, Tsermpini EE, Khasawneh LQ, Sangkuhl K, Duconge J, Botton MR, Savieo J, Nofziger C, Whirl-Carrillo M, Klein TE, Gaedigk A, PharmVar GeneFocus: CYP4F2 Clinical pharmacology and therapeutics116:963-975 2024 |
| PubMed ID: 39135485 |
| |
| Bai X, Chen Z, Chen K, Wu Z, Wang R, Liu J, Chang L, Wen L, Tang F, Simultaneous de novo calling and phasing of genetic variants at chromosome-scale using NanoStrand-seq Cell discovery10:74 2023 |
| PubMed ID: 38977679 |
| |
| Gilpatrick T, Wang JZ, Weiss D, Norris AL, Eshleman J, Timp W, IVT generation of guideRNAs for Cas9-enrichment Nanopore Sequencing bioRxiv : the preprint server for biology10:74 2023 |
| PubMed ID: 36798399 |
| |
| Gimeno-Valiente F, Martín-Arana J, Tébar-Martínez R, Gambardella V, Martínez-Ciarpaglini C, García-Micó B, Martínez-Castedo B, Palomar B, García-Bartolomé M, Seguí V, Huerta M, Moro-Valdezate D, Pla-Martí V, Pérez-Santiago L, Roselló S, Roda D, Cervantes A, Tarazona N, Sequencing paired tumor DNA and white blood cells improves circulating tumor DNA tracking and detects pathogenic germline variants in localized colon cancer ESMO open8:102051 2023 |
| PubMed ID: 37951129 |
| |
| Hansen T, Fong S, Capra JA, Hodges E, Human gene regulatory evolution is driven by the divergence of regulatory element function in both bioRxiv : the preprint server for biology8:102051 2023 |
| PubMed ID: 36824965 |
| |
| Kolekar P, Balagopal V, Dong L, Liu Y, Foy S, Tran Q, Mulder H, Huskey AL, Plyler E, Liang Z, Ma J, Nakitandwe J, Gu J, Namwanje M, Maciaszek J, Payne-Turner D, Mallampati S, Wang L, Easton J, Klco JM, Ma X, SJPedPanel: A pan-cancer gene panel for childhood malignancies medRxiv : the preprint server for health sciences8:102051 2023 |
| PubMed ID: 38076942 |
| |
| Kotlov N, Shaposhnikov K, Tazearslan C, Chasse M, Baisangurov A, Podsvirova S, Fernandez D, Abdou M, Kaneunyenye L, Morgan K, Cheremushkin I, Zemskiy P, Chelushkin M, Sorokina M, Belova E, Khorkova S, Lozinsky Y, Nuzhdina K, Vasileva E, Kravchenko D, Suryamohan K, Nomie K, Curran J, Fowler N, Bagaev A, Procrustes is a machine-learning approach that removes cross-platform batch effects from clinical RNA sequencing data Communications biology7:392 2023 |
| PubMed ID: 38555407 |
| |
| Kvapilova K, Misenko P, Radvanszky J, Brzon O, Budis J, Gazdarica J, Pos O, Korabecna M, Kasny M, Szemes T, Kvapil P, Paces J, Kozmik Z, Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses BMC genomics25:187 2023 |
| PubMed ID: 38365587 |
| |
| Liu MH, Costa B, Choi U, Bandler RC, Lassen E, Gronska-Peski M, Schwing A, Murphy ZR, Rosenkjær D, Picciotto S, Bianchi V, Stengs L, Edwards M, Loh CA, Truong TK, Brand RE, Pastinen T, Wagner JR, Skytte AB, Tabori U, Shoag JE, Evrony GD, Single-strand mismatch and damage patterns revealed by single-molecule DNA sequencing bioRxiv : the preprint server for biology25:187 2023 |
| PubMed ID: 36824744 |
| |
| Longo GMC, Sayols S, Kotini AG, Heinen S, Möckel MM, Beli P, Roukos V, Linking CRISPR-Cas9 double-strand break profiles to gene editing precision with BreakTag Nature biotechnology25:187 2023 |
| PubMed ID: 38740992 |
| |
| Merav M, Bitensky EM, Heilbrun EE, Hacohen T, Kirshenbaum A, Golan-Berman H, Cohen Y, Adar S, Gene architecture is a determinant of the transcriptional response to bulky DNA damages Life science alliance7:187 2023 |
| PubMed ID: 38167611 |
| |
| Scherthan H, Geiger B, Ridinger D, Müller J, Riccobono D, Bestvater F, Port M, Hausmann M, Nano-Architecture of Persistent Focal DNA Damage Regions in the Minipig Epidermis Weeks after Acute ?-Irradiation Biomolecules13:187 2023 |
| PubMed ID: 37892200 |
| |
| Sun J, Su M, Ma J, Xu M, Ma C, Li W, Liu R, He Q, Su Z, Cross-platform comparisons for targeted bisulfite sequencing of MGISEQ-2000 and NovaSeq6000 Clinical epigenetics15:130 2023 |
| PubMed ID: 37582783 |
| |
| Sun Z, Behati S, Wang P, Bhagwate A, McDonough S, Wang V, Taylor W, Cunningham J, Kisiel J, Performance comparisons of methylation and structural variants from low-input whole-genome methylation sequencing Epigenomics15:130 2023 |
| PubMed ID: 36919677 |
| |
| Ueda MT, Inamo J, Miya F, Shimada M, Yamaguchi K, Kochi Y, Functional and dynamic profiling of transcript isoforms reveals essential roles of alternative splicing in interferon response Cell genomics15:100654 2023 |
| PubMed ID: 39288763 |
| |
| Uppuluri L, Shi CH, Varapula D, Young E, Ehrlich RL, Wang Y, Piazza D, Mell JC, Yip KY, Xiao M, A long-read sequencing strategy with overlapping linkers on adjacent fragments (OLAF-Seq) for targeted resequencing and enrichment Scientific reports14:5583 2023 |
| PubMed ID: 38448490 |
| |
| Vozza G, Bonetti E, Tini G, Favalli V, Frigè G, Bucci G, De Summa S, Zanfardino M, Zapelloni F, Mazzarella L, Benchmarking and improving the performance of variant-calling pipelines with RecallME Bioinformatics (Oxford, England)39:5583 2023 |
| PubMed ID: 38092052 |
| |
| Wu B, Li J, Wang H, Liu J, Li J, Sun F, Feng DC, RIPK1 is aberrantly expressed in multiple B-cell cancers and implicated in the underlying pathogenesis Discover Oncology14:131 2023 |
| PubMed ID: 37462822 |
| |
| Xia Y, Katz M, Chandramohan D, Bechor E, Podgursky B, Hoxie M, Zhang Q, Chertman W, Kang J, Blue E, Chen J, Schleede J, Slotnick NR, Du X, Boostanfar R, Urcia E, Behr B, Cohen J, Siddiqui N, The first clinical validation of whole-genome screening on standard trophectoderm biopsies of preimplantation embryos F&S reports5:63-71 2023 |
| PubMed ID: 38524212 |
| |
| Xue JR, Mackay-Smith A, Mouri K, Garcia MF, Dong MX, Akers JF, Noble M, Li X, Zoonomia Consortium† X, Lindblad-Toh K, Karlsson EK, Noonan JP, Capellini TD, Brennand KJ, Tewhey R, Sabeti PC, Reilly SK, The functional and evolutionary impacts of human-specific deletions in conserved elements Science (New York, NY)380:eabn2253 2023 |
| PubMed ID: 37104592 |
| |
| Zollinger DR, Rivers E, Fine A, Huang Y, Son J, Kalyan A, Gray W, Baharian G, Hammond C, Ram R, Ringman L, Hafez D, Savel D, Patel V, Dantone M, Guo C, Childress M, Xu C, Johng D, Wallden B, Pokharel P, Camara W, Hegde PS, Hughes J, Carter C, Davarpanah N, Degaonkar V, Gupta P, Mariathasan S, Powles T, Ferree S, Dennis L, Young A, Analytical validation of a novel comprehensive genomic profiling informed circulating tumor DNA monitoring assay for solid tumors PloS one19:e0302129 2023 |
| PubMed ID: 38753705 |
| |
| Adolfsson E, Kling D, Gunnarsson C, Jonasson J, Gréen H, Gréen A, Whole exome sequencing of FFPE samples-expanding the horizon of forensic molecular autopsies International journal of legal medicine19:e0302129 2022 |
| PubMed ID: 36346469 |
| |
| Bae JH, Liu R, Roberts E, Nguyen E, Tabrizi S, Rhoades J, Blewett T, Xiong K, Gydush G, Shea D, An Z, Patel S, Cheng J, Sridhar S, Liu MH, Lassen E, Skytte AB, Gronska-Peski M, Shoag JE, Evrony GD, Parsons HA, Mayer EL, Makrigiorgos GM, Golub TR, Adalsteinsson VA, Single duplex DNA sequencing with CODEC detects mutations with high sensitivity Nature genetics55:871-879 2022 |
| PubMed ID: 37106072 |
| |
| Battaglia S, Dong K, Wu J, Chen Z, Najm FJ, Zhang Y, Moore MM, Hecht V, Shoresh N, Bernstein BE, Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements Nature genetics54:1504-1513 2022 |
| PubMed ID: 36195755 |
| |
| Chai H, Tjong H, Li P, Liao W, Wang P, Wong CH, Ngan CY, Leonard WJ, Wei CL, Ruan Y, ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs Nature communications14:213 2022 |
| PubMed ID: 36639381 |
| |
| Fazel-Najafabadi M, Rallabandi HR, Singh MK, Maiti GP, Morris J, Looger LL, Nath SK, Discovery and Functional Characterization of Two Regulatory Variants Underlying Lupus Susceptibility at 2p131 Genes13:213 2022 |
| PubMed ID: 35741778 |
| |
| Feng YS, Zhang C, Chen QF, Wang Y, Kang KL, Zhao J, Ji AQ, Ye J, Wang L, Evaluation of the MHSeqTyper47 kit for forensically challenging DNA samples Forensic science international Genetics61:102763 2022 |
| PubMed ID: 35939876 |
| |
| Forgetta V, Li R, Darmond-Zwaig C, Belisle A, Balion C, Roshandel D, Wolfson C, Lettre G, Pare G, Paterson AD, Griffith LE, Verschoor C, Lathrop M, Kirkland S, Raina P, Richards JB, Ragoussis J, Cohort profile: genomic data for 26 622 individuals from the Canadian Longitudinal Study on Aging (CLSA) BMJ open12:e059021 2022 |
| PubMed ID: 35273064 |
| |
| Füllgrabe J, Gosal WS, Creed P, Liu S, Lumby CK, Morley DJ, Ost TWB, Vilella AJ, Yu S, Bignell H, Burns P, Charlesworth T, Fu B, Fordham H, Harding NJ, Gandelman O, Golder P, Hodson C, Li M, Lila M, Liu Y, Mason J, Mellad J, Monahan JM, Nentwich O, Palmer A, Steward M, Taipale M, Vandomme A, San-Bento RS, Singhal A, Vivian J, Wójtowicz N, Williams N, Walker NJ, Wong NCH, Yalloway GN, Holbrook JD, Balasubramanian S, Simultaneous sequencing of genetic and epigenetic bases in DNA Nature biotechnology12:e059021 2022 |
| PubMed ID: 36747096 |
| |
| Hansen TJ, Hodges E, ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome Genome research12:e059021 2022 |
| PubMed ID: 35858748 |
| |
| Inamo J, Suzuki A, Ueda MT, Yamaguchi K, Nishida H, Suzuki K, Kaneko Y, Takeuchi T, Hatano H, Ishigaki K, Ishihama Y, Yamamoto K, Kochi Y, Long-read sequencing for 29 immune cell subsets reveals disease-linked isoforms Nature communications15:4285 2022 |
| PubMed ID: 38806455 |
| |
| Karimnezhad A, Perkins TJ, Empirical Bayes single nucleotide variant-calling for next-generation sequencing data Scientific reports14:1550 2022 |
| PubMed ID: 38233494 |
| |
| Lopes M, Louzada S, Ferreira D, Veríssimo G, Eleutério D, Gama-Carvalho M, Chaves R, Human Satellite 1A analysis provides evidence of pericentromeric transcription BMC biology21:28 2022 |
| PubMed ID: 36755311 |
| |
| Lunke S, Bouffler SE, Patel CV, Sandaradura SA, Wilson M, Pinner J, Hunter MF, Barnett CP, Wallis M, Kamien B, Tan TY, Freckmann ML, Chong B, Phelan D, Francis D, Kassahn KS, Ha T, Gao S, Arts P, Jackson MR, Scott HS, Eggers S, Rowley S, Boggs K, Rakonjac A, Brett GR, de Silva MG, Springer A, Ward M, Stallard K, Simons C, Conway T, Halman A, Van Bergen NJ, Sikora T, Semcesen LN, Stroud DA, Compton AG, Thorburn DR, Bell KM, Sadedin S, North KN, Christodoulou J, Stark Z, Integrated multi-omics for rapid rare disease diagnosis on a national scale Nature medicine29:1681-1691 2022 |
| PubMed ID: 37291213 |
| |
| Masset H, Ding J, Dimitriadou E, Debrock S, Tšuiko O, Smits K, Peeraer K, Voet T, Zamani Esteki M, Vermeesch JR, Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing Nucleic acids research50:e63 2022 |
| PubMed ID: 35212381 |
| |
| McClinton B, Watson CM, Crinnion LA, McKibbin M, Ali M, Inglehearn CF, Toomes C, Haplotyping Using Long-Range PCR and Nanopore Sequencing of Phase Variants; Lessons Learned From the ABCA4 Locus Laboratory investigation; a journal of technical methods and pathology50:100160 2022 |
| PubMed ID: 37088464 |
| |
| Ng JK, Vats P, Fritz-Waters E, Sarkar S, Sams EI, Padhi EM, Payne ZL, Leonard S, West MA, Prince C, Trani L, Jansen M, Vacek G, Samadi M, Harkins TT, Pohl C, Turner TN, de novo variant calling identifies cancer mutation signatures in the 1000 Genomes Project Human mutation50:100160 2022 |
| PubMed ID: 36054329 |
| |
| Nuwan C. Hettige, Huashan Peng, Hanrong Wu, Xin Zhang, Volodymyr Yerko, Ying Zhang, Malvin Jefri, Vincent Soubannier, Gilles Maussion, Shaima Alsuwaidi, Anjie Ni, Cecilia Rocha, Jeyashree Krishnan, Vincent McCarty, Lilit Antonyan, Andreas Schuppert, Gustavo Turecki, Edward A. Fon, Thomas M. Durcan, Carl Ernst, A protocol for full-rotation soft X-ray tomography of single cells 3519903917:475-488 2022 |
| PubMed ID: 35199039 |
| |
| Parteka-Tojek Z, Zhu JJ, Lee B, Jodkowska K, Wang P, Aaron J, Chew TL, Banecki K, Plewczynski D, Ruan Y, Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy Scientific reports12:8582 2022 |
| PubMed ID: 35595799 |
| |
| Ramirez D, B Chuong E, D Dowell R, Nascent transcription upon interferon-a2 stimulation on human and rhesus macaque lymphoblastoid cell lines BMC research notes16:292 2022 |
| PubMed ID: 37885027 |
| |
| Shum EY, Lai JH, Li S, Lee HG, Soliman J, Raol VK, Lee CK, Fodor SPA, Fan HC, Next-Generation Digital Polymerase Chain Reaction: High-Dynamic-Range Single-Molecule DNA Counting via Ultrapartitioning Analytical chemistry94:17868-17876 2022 |
| PubMed ID: 36508568 |
| |
| Sinitcyn P, Richards AL, Weatheritt RJ, Brademan DR, Marx H, Shishkova E, Meyer JG, Hebert AS, Westphall MS, Blencowe BJ, Cox J, Coon JJ, Global detection of human variants and isoforms by deep proteome sequencing Nature biotechnology94:17868-17876 2022 |
| PubMed ID: 36959352 |
| |
| Steiert TA, Fuß J, Juzenas S, Wittig M, Hoeppner MP, Vollstedt M, Varkalaite G, ElAbd H, Brockmann C, Görg S, Gassner C, Forster M, Franke A, High-throughput method for the hybridisation-based targeted enrichment of long genomic fragments for PacBio third-generation sequencing NAR genomics and bioinformatics4:lqac051 2022 |
| PubMed ID: 35855323 |
| |
| Tilleman L, Rubben K, Van Criekinge W, Deforce D, Van Nieuwerburgh F, Haplotyping pharmacogenes using TLA combined with Illumina or Nanopore sequencing Scientific reports12:17734 2022 |
| PubMed ID: 36273027 |
| |
| Vollger MR, Dishuck PC, Harvey WT, DeWitt WS, Guitart X, Goldberg ME, Rozanski AN, Lucas J, Asri M, Human Pangenome Reference Consortium M, Munson KM, Lewis AP, Hoekzema K, Logsdon GA, Porubsky D, Paten B, Harris K, Hsieh P, Eichler EE, Increased mutation and gene conversion within human segmental duplications Nature617:325-334 2022 |
| PubMed ID: 37165237 |
| |
| Wen J, Trost B, Engchuan W, Halvorsen M, Pallotto LM, Mitina A, Ancalade N, Farrell M, Backstrom I, Guo K, Pellecchia G, Thiruvahindrapuram B, Giusti-Rodriguez P, Rosen JD, Li Y, Won H, Magnusson PKE, Gyllensten U, Bassett AS, Hultman CM, Sullivan PF, Yuen RKC, Szatkiewicz JP, Rare tandem repeat expansions associate with genes involved in synaptic and neuronal signaling functions in schizophrenia Molecular psychiatry28:475-482 2022 |
| PubMed ID: 36380236 |
| |
| Wright S, Zhao X, Rosikiewicz W, Mryncza S, Hyle J, Qi W, Liu Z, Yi S, Cheng Y, Xu B, Li C, Systematic characterization of the HOXA9 downstream targets in MLL-r leukemia by noncoding CRISPR screens Nature communications14:7464 2022 |
| PubMed ID: 38016946 |
| |
| Xu N, Shi W, Cao X, Zhou X, Jin L, Huang HF, Chen S, Xu C, Parental mosaicism detection and preimplantation genetic testing in families with multiple transmissions of de novo mutations Journal of medical genetics14:7464 2022 |
| PubMed ID: 36707240 |
| |
| Yan B, Wang D, Vaisvila R, Sun Z, Ettwiller L, Methyl-SNP-seq reveals dual readouts of methylome and variome at molecule resolution while enabling target enrichment Genome research32:2079-2091 2022 |
| PubMed ID: 36332968 |
| |
| Yao X, Zhou Z, Xie Y, Huang Z, Lu S, Liu C, Wang J, Li X, Methodology established for the detection of circulating tumor DNA by hybridization capture BioTechniques73:151-158 2022 |
| PubMed ID: 36065956 |
| |
| Zhong JY, Niu L, Lin ZB, Bai X, Chen Y, Luo F, Hou C, Xiao CL, High-throughput Pore-C reveals the single-allele topology and cell type-specificity of 3D genome folding Nature communications14:1250 2022 |
| PubMed ID: 36878904 |
| |
| Barnes AB, Keener RM, Schott BH, Wang L, Valdivia RH, Ko DC, Human genetic diversity regulating the HGG advances3:100071 2021 |
| PubMed ID: 35047856 |
| |
| Caballero M, Ge T, Rebelo AR, Seo S, Kim S, Brooks K, Zuccaro M, Kanagaraj R, Vershkov D, Kim D, Smogorzewska A, Smolka M, Benvenisty N, West SC, Egli D, Mace EM, Koren A, Comprehensive analysis of DNA replication timing across 184 cell lines suggests a role for MCM10 in replication timing regulation Human molecular genetics3:100071 2021 |
| PubMed ID: 35394024 |
| |
| Chiu R, Rajan-Babu IS, Birol I, Friedman JM, Linked-read sequencing for detecting short tandem repeat expansions Scientific reports12:9352 2021 |
| PubMed ID: 35672336 |
| |
| De Witte L, Raman L, Baetens M, De Koker A, Callewaert N, Symoens S, Tilleman K, Vanden Meerschaut F, Dheedene A, Menten B, GENType: all-in-one preimplantation genetic testing by pedigree haplotyping and copy number profiling suitable for third-party reproduction Human reproduction (Oxford, England)37:1678-1691 2021 |
| PubMed ID: 35552408 |
| |
| Dubé MP, Lemaçon A, Barhdadi A, Lemieux Perreault LP, Oussaïd E, Asselin G, Provost S, Sun M, Sandoval J, Legault MA, Mongrain I, Dubois A, Valois D, Dedelis E, Lousky J, Choi J, Goulet E, Savard C, Chicoine LM, Cossette M, Chabot-Blanchet M, Guertin MC, de Denus S, Bouabdallaoui N, Marchand R, Bassevitch Z, Nozza A, Gaudet D, L'Allier PL, Hussin J, Boivin G, Busseuil D, Tardif JC, Genetics of symptom remission in outpatients with COVID-19 Scientific reports11:10847 2021 |
| PubMed ID: 34035401 |
| |
| Foox J, Nordlund J, Lalancette C, Gong T, Lacey M, Lent S, Langhorst BW, Ponnaluri VKC, Williams L, Padmanabhan KR, Cavalcante R, Lundmark A, Butler D, Mozsary C, Gurvitch J, Greally JM, Suzuki M, Menor M, Nasu M, Alonso A, Sheridan C, Scherer A, Bruinsma S, Golda G, Muszynska A, Labaj PP, Campbell MA, Wos F, Raine A, Liljedahl U, Axelsson T, Wang C, Chen Z, Yang Z, Li J, Yang X, Wang H, Melnick A, Guo S, Blume A, Franke V, Ibanez de Caceres I, Rodriguez-Antolin C, Rosas R, Davis JW, Ishii J, Megherbi DB, Xiao W, Liao W, Xu J, Hong H, Ning B, Tong W, Akalin A, Wang Y, Deng Y, Mason CE, The SEQC2 epigenomics quality control (EpiQC) study Genome biology22:332 2021 |
| PubMed ID: 34872606 |
| |
| Hanlon VCT, Chan DD, Hamadeh Z, Wang Y, Mattsson CA, Spierings DCJ, Coope RJN, Lansdorp PM, Construction of Strand-seq libraries in open nanoliter arrays Cell reports methods2:100150 2021 |
| PubMed ID: 35474869 |
| |
| Huang M, Yang Y, Wen X, Xu W, Lu N, Sun X, Tu J, Lu Z, Inferring single cell expression profiles from overlapped pooling sequencing data with compressed sensing strategy Nucleic acids research2:100150 2021 |
| PubMed ID: 34244789 |
| |
| Kim KL, van Galen P, Hovestadt V, Rahme GJ, Andreishcheva EN, Shinde A, Gaskell E, Jones DR, Shema E, Bernstein BE, Systematic detection of m Cell reports methods1:100150 2021 |
| PubMed ID: 34734208 |
| |
| Klein SG, Alsolami SM, Arossa S, Ramos-Mandujano G, Parry AJ, Steckbauer A, Duarte CM, Li M, In situ monitoring reveals cellular environmental instabilities in human pluripotent stem cell culture Communications biology5:119 2021 |
| PubMed ID: 35136190 |
| |
| Lang J, Sun J, Yang Z, He L, He Y, Chen Y, Huang L, Li P, Li J, Qin L, Nano2NGS-Muta: a framework for converting nanopore sequencing data to NGS-liked sequencing data for hotspot mutation detection NAR genomics and bioinformatics4:lqac033 2021 |
| PubMed ID: 35464239 |
| |
| Lin JH, Chen S, Pallavajjala A, Guedes LB, Lotan TL, Bacher JW, Eshleman JR, Validation of Long Mononucleotide Repeat Markers for Detection of Microsatellite Instability The Journal of molecular diagnostics : JMD24:144-157 2021 |
| PubMed ID: 34864149 |
| |
| Liu Z, Naler LB, Zhu Y, Deng C, Zhang Q, Zhu B, Zhou Z, Sarma M, Murray A, Xie H, Lu C, nMOWChIP-seq: low-input genome-wide mapping of non-histone targets NAR genomics and bioinformatics4:lqac030 2021 |
| PubMed ID: 35402909 |
| |
| Llimos G, Gardeux V, Koch U, Kribelbauer JF, Hafner A, Alpern D, Pezoldt J, Litovchenko M, Russeil J, Dainese R, Moia R, Mahmoud AM, Rossi D, Gaidano G, Plass C, Lutsik P, Gerhauser C, Waszak SM, Boettiger A, Radtke F, Deplancke B, A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation Nature communications13:2042 2021 |
| PubMed ID: 35440565 |
| |
| Marasco LE, Dujardin G, Sousa-Luís R, Liu YH, Stigliano JN, Nomakuchi T, Proudfoot NJ, Krainer AR, Kornblihtt AR, Counteracting chromatin effects of a splicing-correcting antisense oligonucleotide improves its therapeutic efficacy in spinal muscular atrophy Cell185:2057-2070.e15 2021 |
| PubMed ID: 35688133 |
| |
| Massey DJ, Koren A, High-throughput analysis of single human cells reveals the complex nature of DNA replication timing control Nature communications13:2402 2021 |
| PubMed ID: 35504890 |
| |
| McDonald TL, Zhou W, Castro CP, Mumm C, Switzenberg JA, Mills RE, Boyle AP, Cas9 targeted enrichment of mobile elements using nanopore sequencing Nature communications12:3586 2021 |
| PubMed ID: 34117247 |
| |
| Pan N, Chen S, Cai X, Li J, Yu T, Huang HF, Zhang J, Xu C, Low-level germline mosaicism of a novel SMARCA2 missense variant: Expanding the phenotypic spectrum and mode of genetic transmission Molecular genetics & genomic medicine12:e1763 2021 |
| PubMed ID: 34296532 |
| |
| Peng R, Zhang R, Li J, Continual Improvement of the Reliability of Next-Generation Sequencing-Based ctDNA Analysis: A Long-Term Comparison of ctDNA Detection in China Clinical chemistry68:940-952 2021 |
| PubMed ID: 35687601 |
| |
| Porubsky D, Höps W, Ashraf H, Hsieh P, Rodriguez-Martin B, Yilmaz F, Ebler J, Hallast P, Maria Maggiolini FA, Harvey WT, Henning B, Audano PA, Gordon DS, Ebert P, Hasenfeld P, Benito E, Zhu Q, Human Genome Structural Variation Consortium (HGSVC) Q, Lee C, Antonacci F, Steinrücken M, Beck CR, Sanders AD, Marschall T, Eichler EE, Korbel JO, Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders Cell68:940-952 2021 |
| PubMed ID: 35525246 |
| |
| Rehder C, Bean LJH, Bick D, Chao E, Chung W, Das S, O'Daniel J, Rehm H, Shashi V, Vincent LM, ACMG Laboratory Quality Assurance Committee LM, Next-generation sequencing for constitutional variants in the clinical laboratory, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG) Genetics in medicine : official journal of the American College of Medical Genetics23:1399-1415 2021 |
| PubMed ID: 33927380 |
| |
| Ribarska T, Bjørnstad PM, Sundaram AYM, Gilfillan GD, Optimization of enzymatic fragmentation is crucial to maximize genome coverage: a comparison of library preparation methods for Illumina sequencing BMC genomics23:92 2021 |
| PubMed ID: 35105301 |
| |
| Sanders JT, Golloshi R, Das P, Xu Y, Terry PH, Nash DG, Dekker J, McCord RP, Loops, topologically associating domains, compartments, and territories are elastic and robust to dramatic nuclear volume swelling Scientific reports12:4721 2021 |
| PubMed ID: 35304523 |
| |
| Scheiper-Welling S, Körber S, Geisen C, Verhoff MA, Kauferstein S, Genetic analysis of sudden unexpected death cases: Evaluation of library preparation methods to handle heterogeneous sample material Forensic science international322:110768 2021 |
| PubMed ID: 33774385 |
| |
| Shi J, Tan P, Han D, Zhang R, Li J, Zhang R, Non-invasive prenatal screening for foetal trisomy: An assessment of reliability and reporting Clinical biochemistry100:71-77 2021 |
| PubMed ID: 34843730 |
| |
| Shi Z, Lopez J, Kalliney W, Sutton B, Simpson J, Maggert K, Liu S, Wan J, Stack MS, Development and evaluation of ActSeq: A targeted next-generation sequencing panel for clinical oncology use PloS one17:e0266914 2021 |
| PubMed ID: 35446881 |
| |
| Sicko RJ, Stevens CF, Hughes EE, Leisner M, Ling H, Saavedra-Matiz CA, Caggana M, Kay DM, Validation of a Custom Next-Generation Sequencing Assay for Cystic Fibrosis Newborn Screening International journal of neonatal screening7:e0266914 2021 |
| PubMed ID: 34842611 |
| |
| Tanic M, Moghul I, Rodney S, Dhami P, Vaikkinen H, Ambrose J, Barrett J, Feber A, Beck S, Comparison and imputation-aided integration of five commercial platforms for targeted DNA methylome analysis Nature biotechnology7:e0266914 2021 |
| PubMed ID: 35654977 |
| |
| Tu J, Duan M, Liu W, Lu N, Zhou Y, Sun X, Lu Z, Direct genome-wide identification of G-quadruplex structures by whole-genome resequencing Nature communications12:6014 2021 |
| PubMed ID: 34650044 |
| |
| Uppuluri L, Wang Y, Young E, Wong JS, Abid HZ, Xiao M, Multiplex structural variant detection by whole-genome mapping and nanopore sequencing Scientific reports12:6512 2021 |
| PubMed ID: 35444207 |
| |
| Wadden J, Newell BS, Bugbee J, John V, Bruzek AK, Dickson RP, Koschmann C, Blaauw D, Narayanasamy S, Das R, Ultra-rapid somatic variant detection via real-time targeted amplicon sequencing Communications biology5:708 2021 |
| PubMed ID: 35840782 |
| |
| Wang Z, Guo R, Trudeau SJ, Wolinsky E, Ast T, Liang JH, Jiang C, Ma Y, Teng M, Mootha VK, Gewurz BE, CYB561A3 is the key lysosomal iron reductase required for Burkitt B-cell growth and survival Blood138:2216-2230 2021 |
| PubMed ID: 34232987 |
| |
| Wei X, Xiang Y, Peters DT, Marius C, Sun T, Shan R, Ou J, Lin X, Yue F, Li W, Southerland KW, Diao Y, HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization Molecular cell82:1225-1238.e6 2021 |
| PubMed ID: 35196517 |
| |
| Zhang H, Rice ME, Alvin JW, Farrera-Gaffney D, Galligan JJ, Johnson MDL, Cusanovich DA, Extensive evaluation of ATAC-seq protocols for native or formaldehyde-fixed nuclei BMC genomics23:214 2021 |
| PubMed ID: 35296236 |
| |
| Zhou G, Zhou M, Zeng F, Zhang N, Sun Y, Qiao Z, Guo X, Zhou S, Yun G, Xie J, Wang X, Liu F, Fan C, Wang Y, Fang Z, Tian Z, Dai W, Sun J, Peng Z, Song L, Performance characterization of PCR-free whole genome sequencing for clinical diagnosis Medicine101:e28972 2021 |
| PubMed ID: 35451387 |
| |
| Akolkar D, Patil D, Srivastava N, Patil R, Datta V, Apurwa S, Yashwante N, Dhasarathan R, Gosavi R, John J, Khan S, Jadhav N, Mene P, Ahire D, Pawar S, Bodke H, Sahoo S, Nile A, Saindane D, Darokar H, Devhare P, Srinivasan A, Datar R, Development and validation of a multigene variant profiling assay to guide targeted and immuno therapy selection in solid tumors PloS one16:e0246048 2020 |
| PubMed ID: 33556149 |
| |
| Barrett SR, Hoffman NG, Rosenthal C, Bryan A, Marshall DA, Lieberman J, Greninger AL, Peddu V, Cookson BT, Salipante SJ, Sensitive identification of bacterial DNA in clinical specimens by broad range 16S rRNA enrichment Journal of clinical microbiology16:e0246048 2020 |
| PubMed ID: 33028602 |
| |
| Budde BS, Aly MA, Mohamed MR, Breß A, Altmüller J, Motameny S, Kawalia A, Thiele H, Konrad K, Becker C, Toliat MR, Nürnberg G, Said EA, Mohamed ES, Pfister M, Nürnberg P, Comprehensive molecular analysis of 61 Egyptian families with hereditary nonsyndromic hearing loss Clinical genetics16:e0246048 2020 |
| PubMed ID: 32279305 |
| |
| Cheasley D, Devereux L, Hughes S, Nickson C, Procopio P, Lee G, Li N, Pridmore V, Elder K, Bruce Mann G, Kader T, Rowley SM, Fox SB, Byrne D, Saunders H, Fujihara KM, Lim B, Gorringe KL, Campbell IG, The TP53 mutation rate differs in breast cancers that arise in women with high or low mammographic density NPJ breast cancer6:34 2020 |
| PubMed ID: 32802943 |
| |
| Cheasley D, Nigam A, Zethoven M, Hunter S, Etemadmoghadam D, Semple T, Allan P, Carey MS, Fernandez ML, Dawson A, Köbel M, Huntsman DG, Page CL, Mes-Masson AM, Provencher D, Hacker N, Gao Y, Bowtell D, de Fazio A, Gorringe KL, Campbell IG, Genomic analysis of low-grade serous ovarian carcinoma to identify key drivers and therapeutic vulnerabilities The Journal of pathology6:34 2020 |
| PubMed ID: 32901952 |
| |
| Conconi D, Redaelli S, Lissoni AA, Cilibrasi C, Perego P, Gautiero E, Sala E, Paderno M, Dalprà L, Landoni F, Lavitrano M, Roversi G, Bentivegna A, Genomic and Epigenomic Profile of Uterine Smooth Muscle Tumors of Uncertain Malignant Potential (STUMPs) Revealed Similarities and Differences with Leiomyomas and Leiomyosarcomas International journal of molecular sciences22:34 2020 |
| PubMed ID: 33557274 |
| |
| Deng C, Murphy TW, Zhang Q, Naler LB, Xu A, Lu C, Multiplexed and Ultralow-Input ChIP-seq Enabled by Tagmentation-Based Indexing and Facile Microfluidics Analytical chemistry22:34 2020 |
| PubMed ID: 32957776 |
| |
| Dong Z, Chau MHK, Zhang Y, Yang Z, Shi M, Wah YM, Kwok YK, Leung TY, Morton CC, Choy KW, Low-pass genome sequencing-based detection of absence of heterozygosity: validation in clinical cytogenetics Genetics in medicine : official journal of the American College of Medical Genetics23:1225-1233 2020 |
| PubMed ID: 33772221 |
| |
| Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R, Yilmaz F, Zhao X, Hsieh P, Lee J, Kumar S, Lin J, Rausch T, Chen Y, Ren J, Santamarina M, Höps W, Ashraf H, Chuang NT, Yang X, Munson KM, Lewis AP, Fairley S, Tallon LJ, Clarke WE, Basile AO, Byrska-Bishop M, Corvelo A, Evani US, Lu TY, Chaisson MJP, Chen J, Li C, Brand H, Wenger AM, Ghareghani M, Harvey WT, Raeder B, Hasenfeld P, Regier AA, Abel HJ, Hall IM, Flicek P, Stegle O, Gerstein MB, Tubio JMC, Mu Z, Li YI, Shi X, Hastie AR, Ye K, Chong Z, Sanders AD, Zody MC, Talkowski ME, Mills RE, Devine SE, Lee C, Korbel JO, Marschall T, Eichler EE, Haplotype-resolved diverse human genomes and integrated analysis of structural variation Science (New York, NY)372:1225-1233 2020 |
| PubMed ID: 33632895 |
| |
| Goodwin PJ, Dowling RJO, Ennis M, Chen BE, Parulekar WR, Shepherd LE, Burnell MJ, Vander Meer R, Molckovsky A, Gurjal A, Gelmon KA, Ligibel JA, Hershman DL, Mayer IA, Whelan TJ, Hobday TJ, Rastogi P, Rabaglio-Poretti M, Lemieux J, Thompson AM, Rea DW, Stambolic V, NPJ breast cancer7:74 2020 |
| PubMed ID: 34103538 |
| |
| Gorla A, Jew B, Zhang L, Sul JH, xGAP: A python based efficient, modular, extensible and fault tolerant genomic analysis pipeline for variant discovery Bioinformatics (Oxford, England)7:74 2020 |
| PubMed ID: 33416856 |
| |
| Granja JM, Corces MR, Pierce SE, Bagdatli ST, Choudhry H, Chang HY, Greenleaf WJ, ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis Nature genetics53:403-411 2020 |
| PubMed ID: 33633365 |
| |
| Graybuck LT, Daigle TL, Sedeño-Cortés AE, Walker M, Kalmbach B, Lenz GH, Morin E, Nguyen TN, Garren E, Bendrick JL, Kim TK, Zhou T, Mortrud M, Yao S, Siverts LA, Larsen R, Gore BB, Szelenyi ER, Trader C, Balaram P, van Velthoven CTJ, Chiang M, Mich JK, Dee N, Goldy J, Cetin AH, Smith K, Way SW, Esposito L, Yao Z, Gradinaru V, Sunkin SM, Lein E, Levi BP, Ting JT, Zeng H, Tasic B, Enhancer viruses for combinatorial cell-subclass-specific labeling Neuron109:1449-1464.e13 2020 |
| PubMed ID: 33789083 |
| |
| Harkins KM, Schaefer NK, Troll CJ, Rao V, Kapp J, Naughton C, Shapiro B, Green RE, A novel NGS library preparation method to characterize native termini of fragmented DNA Nucleic acids research109:1449-1464.e13 2020 |
| PubMed ID: 32112100 |
| |
| Köffer J, Scheiper-Welling S, Verhoff MA, Bajanowski T, Kauferstein S, Post-mortem genetic investigation of cardiac disease-associated genes in sudden infant death syndrome (SIDS) cases International journal of legal medicine109:1449-1464.e13 2020 |
| PubMed ID: 32789579 |
| |
| Koren A, Massey DJ, Bracci AN, TIGER: inferring DNA replication timing from whole-genome sequence data Bioinformatics (Oxford, England)109:1449-1464.e13 2020 |
| PubMed ID: 33704387 |
| |
| Lee JD, Paulo JA, Posey RR, Mugoni V, Kong NR, Cheloni G, Lee YR, Slack FJ, Tenen DG, Clohessy JG, Gygi SP, Pandolfi PP, Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia Nature methods18:293-302 2020 |
| PubMed ID: 33649590 |
| |
| McKerrow W, Tang Z, Steranka JP, Payer LM, Boeke JD, Keefe D, Fenyö D, Burns KH, Liu C, Human transposon insertion profiling by sequencing (TIPseq) to map LINE-1 insertions in single cells Philosophical transactions of the Royal Society of London Series B, Biological sciences375:20190335 2020 |
| PubMed ID: 32075555 |
| |
| Min YK, Lee YK, Nam SH, Kim JK, Park KS, Kim JW, Quantitative and Qualitative QC of Next-Generation Sequencing for Detecting Somatic Variants: An Example of Detecting Clonal Hematopoiesis of Indeterminate Potential Clinical chemistry375:20190335 2020 |
| PubMed ID: 32395759 |
| |
| Ormond C, Ryan NM, Corvin A, Heron EA, Converting single nucleotide variants between genome builds: from cautionary tale to solution Briefings in bioinformatics375:20190335 2020 |
| PubMed ID: 33822888 |
| |
| Park K, Tran H, Eng KW, Ramazanoglu S, Marrero Rolon RM, Scognamiglio T, Borczuk A, Mosquera JM, Pan Q, Sboner A, Rubin MA, Elemento O, Rennert H, Fernandes H, Song W, Performance Characteristics of a Targeted Sequencing Platform for Simultaneous Detection of Single Nucleotide Variants, Insertions/Deletions, Copy Number Alterations, and Gene Fusions in Cancer Genome Archives of pathology & laboratory medicine375:20190335 2020 |
| PubMed ID: 32045275 |
| |
| Parsons HA, Rhoades J, Reed SC, Gydush G, Ram P, Exman P, Xiong K, Lo CC, Li T, Fleharty M, Kirkner GJ, Rotem D, Cohen O, Yu F, Fitarelli-Kiehl M, Leong KW, Hughes ME, Rosenberg SM, Collins LC, Miller KD, Blumenstiel B, Trippa L, Cibulskis C, Neuberg DS, DeFelice M, Freeman SS, Lennon NJ, Wagle N, Ha G, Stover DG, Choudhury AD, Getz G, Winer EP, Meyerson M, Lin NU, Krop I, Love JC, Makrigiorgos GM, Partridge AH, Mayer EL, Golub TR, Adalsteinsson V, Sensitive detection of minimal residual disease in patients treated for early-stage breast cancer Clinical cancer research : an official journal of the American Association for Cancer Research375:20190335 2020 |
| PubMed ID: 32170028 |
| |
| Payne A, Holmes N, Clarke T, Munro R, Debebe BJ, Loose M, Readfish enables targeted nanopore sequencing of gigabase-sized genomes Nature biotechnology375:20190335 2020 |
| PubMed ID: 33257864 |
| |
| Plongthongkum N, Diep D, Chen S, Lake BB, Zhang K, Scalable dual-omics profiling with single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-seq2) Nature protocols16:4992-5029 2020 |
| PubMed ID: 34650278 |
| |
| Psyrri A, Gkotzamanidou M, Papaxoinis G, Krikoni L, Economopoulou P, Kotsantis I, Anastasiou M, Souliotis VL, The DNA damage response network in the treatment of head and neck squamous cell carcinoma ESMO open6:100075 2020 |
| PubMed ID: 33714009 |
| |
| Ramudo-Cela L, López-Martí JM, Colmeiro-Echeberría D, De-Uña-Iglesias D, Santomé-Collazo JL, Monserrat-Iglesias L, Development and validation of a next-generation sequencing panel for clinical pharmacogenetics Farmacia hospitalaria : organo oficial de expresion cientifica de la Sociedad Espanola de Farmacia Hospitalaria44:243-253 2020 |
| PubMed ID: 33156743 |
| |
| Ray JP, de Boer CG, Fulco CP, Lareau CA, Kanai M, Ulirsch JC, Tewhey R, Ludwig LS, Reilly SK, Bergman DT, Engreitz JM, Issner R, Finucane HK, Lander ES, Regev A, Hacohen N, Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features Nature communications11:1237 2020 |
| PubMed ID: 32144282 |
| |
| Ren H, Xi Y, Li Z, Zhang D, Huang F, Fang X, Zhao X, Zhang X, Chen A, Chen T, Jiang Y, Novel target capture DNA library preparation method using CircLigase-mediated hook ligation New biotechnology59:44-50 2020 |
| PubMed ID: 32688061 |
| |
| Schwessinger R, Gosden M, Downes D, Brown RC, Oudelaar AM, Telenius J, Teh YW, Lunter G, Hughes JR, DeepC: predicting 3D genome folding using megabase-scale transfer learning Nature methods17:1118-1124 2020 |
| PubMed ID: 33046896 |
| |
| Scott SA, Scott ER, Seki Y, Chen AJ, Wallsten R, Owusu Obeng A, Botton MR, Cody N, Shi H, Zhao G, Brake P, Nicoletti P, Yang Y, Delio M, Shi L, Kornreich R, Schadt EE, Edelmann L, Development and Analytical Validation of a 29 Gene Clinical Pharmacogenetic Genotyping Panel: Multi-Ethnic Allele and Copy Number Variant Detection Clinical and translational science14:204-213 2020 |
| PubMed ID: 32931151 |
| |
| Sekar S, Tomasini L, Proukakis C, Bae T, Manlove L, Jang Y, Scuderi S, Zhou B, Kalyva M, Amiri A, Mariani J, Sedlazeck FJ, Urban AE, Vaccarino FM, Abyzov A, Complex mosaic structural variations in human fetal brains Genome research14:204-213 2020 |
| PubMed ID: 33122304 |
| |
| Shanmugam A, Hariharan AK, Hasina R, Nair JR, Katragadda S, Irusappan S, Ravichandran A, Veeramachaneni V, Bettadapura R, Bhati M, Ramaswamy V, Rao VUS, Bagadia RK, Manjunath A, Manjunath NML, Solomon MC, Maji S, Bahadur U, Bettegowda C, Papadopoulos N, Lingen MW, Hariharan R, Gupta V, Agrawal N, Izumchenko E, Ultrasensitive detection of tumor-specific mutations in saliva of patients with oral cavity squamous cell carcinoma Cancer127:1576-1589 2020 |
| PubMed ID: 33405231 |
| |
| Singh B, Maiti GP, Zhou X, Fazel-Najafabadi M, Bae SC, Sun C, Terao C, Okada Y, Heng Chua K, Kochi Y, Guthridge JM, Zhang H, Weirauch M, James JA, Harley JB, Varshney GK, Looger LL, Nath SK, Lupus Susceptibility Region Containing CDKN1B rs34330 Mechanistically Influences Expression and Function of Multiple Target Genes, Also Linked to Proliferation and Apoptosis Arthritis & rheumatology (Hoboken, NJ)73:2303-2313 2020 |
| PubMed ID: 33982894 |
| |
| Söderhäll C, Reinius LE, Salmenperä P, Gentile M, Acevedo N, Konradsen JR, Nordlund B, Hedlin G, Scheynius A, Myllykangas S, Kere J, High-resolution targeted bisulfite sequencing reveals blood cell type-specific DNA methylation patterns in IL13 and ORMDL3 Clinical epigenetics13:106 2020 |
| PubMed ID: 33971943 |
| |
| Trinchant NM, MacKay MJ, Chin C, Afshinnekoo E, Foox J, Meydan C, Butler D, Mozsary C, Vernice NA, Darby C, Schatz MC, Bailey SM, Melnick AM, Guzman M, Bolton K, Braunstein LZ, Garrett-Bakelman F, Levine RL, Hassane D, Mason CE, Clonal Hematopoiesis Before, During, and After Human Spaceflight Cell reports13:108458 2020 |
| PubMed ID: 33242405 |
| |
| Ullmann R, Becker BV, Rothmiller S, Schmidt A, Thiermann H, Kaatsch HL, Schrock G, Müller J, Jakobi J, Obermair R, Port M, Scherthan H, Genomic Adaption and Mutational Patterns in a HaCaT Subline Resistant to Alkylating Agents and Ionizing Radiation International journal of molecular sciences22:108458 2020 |
| PubMed ID: 33498964 |
| |
| Uppugunduri CRS, Huezo-Diaz Curtis P, Nava T, Rezgui MA, Mlakar V, Mlakar SJ, Waespe N, Théoret Y, Gumy-Pause F, Bernard F, Chalandon Y, Boelens JJ, Bredius RGM, Dalle JH, Nath C, Corbacioglu S, Peters C, Bader P, Shaw P, Bittencourt H, Krajinovic M, Ansari M, Association study of candidate DNA-repair gene variants and acute graft versus host disease in pediatric patients receiving allogeneic hematopoietic stem-cell transplantation The pharmacogenomics journal22:9-18 2020 |
| PubMed ID: 34711928 |
| |
| Verma S, Moore MW, Ringler R, Ghosal A, Horvath K, Naef T, Anvari S, Cotter PD, Gunn S, Analytical performance evaluation of a commercial next generation sequencing liquid biopsy platform using plasma ctDNA, reference standards, and synthetic serial dilution samples derived from normal plasma BMC cancer20:945 2020 |
| PubMed ID: 33004033 |
| |
| Wong KHY, Ma W, Wei CY, Yeh EC, Lin WJ, Wang EHF, Su JP, Hsieh FJ, Kao HJ, Chen HH, Chow SK, Young E, Chu C, Poon A, Yang CF, Lin DS, Hu YF, Wu JY, Lee NC, Hwu WL, Boffelli D, Martin D, Xiao M, Kwok PY, Towards a reference genome that captures global genetic diversity Nature communications11:5482 2020 |
| PubMed ID: 33127893 |
| |
| Xu M, Guo L, Gu S, Wang O, Zhang R, Peters BA, Fan G, Liu X, Xu X, Deng L, Zhang Y, TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads GigaScience9:5482 2020 |
| PubMed ID: 32893860 |
| |
| Zeng Q, Leach NT, Zhou Z, Zhu H, Smith JA, Rosenblum LS, Kenyon A, Heim RA, Eisenberg M, Letovsky S, Okamoto PM, A customized scaffolds approach for the detection and phasing of complex variants by next-generation sequencing Scientific reports10:15060 2020 |
| PubMed ID: 32929119 |
| |
| Zhou J, Zhang M, Li X, Wang Z, Pan D, Shi Y, Performance comparison of four types of target enrichment baits for exome DNA sequencing Hereditas158:10 2020 |
| PubMed ID: 33597004 |
| |
| Zhu Y, Cao Z, Lu C, Microfluidic MeDIP-seq for low-input methylomic analysis of mammary tumorigenesis in mice The Analyst144:1904-1915 2020 |
| PubMed ID: 30631869 |
| |
| Asakawa T, Fujii A, Yoneda N, Ohta A, Asakawa H, Enhanced Aggregation of Stimuli Responsive Surfactants by Esterolytic Reactions Journal of oleo science68:573-580 2019 |
| PubMed ID: 31092800 |
| |
| Atkins A, Gupta P, Zhang BM, Tsai WS, Lucas J, Javey M, Vora A, Mei R, Detection of Circulating Tumor DNA with a Single-Molecule Sequencing Analysis Validated for Targeted and Immunotherapy Selection Molecular diagnosis & therapy68:573-580 2019 |
| PubMed ID: 31209714 |
| |
| Azad AK, Huang CK, Jin H, Zou H, Yanakakis L, Du J, Fiddler M, Naeem R, Goldstein Y, Enhanced Carrier Screening for Spinal Muscular Atrophy: Detection of Silent (SMN1: 2 + 0) Carriers Utilizing a Novel TaqMan Genotyping Method Laboratory medicine68:573-580 2019 |
| PubMed ID: 31875889 |
| |
| Bullerwell CE, Robichaud PP, Deprez PML, Joy AP, Wajnberg G, D'Souza D, Chacko S, Fournier S, Crapoulet N, Barnett DA, Lewis SM, Ouellette RJ, EBF1 drives hallmark B cell gene expression by enabling the interaction of PAX5 with the MLL H3K4 methyltransferase complex Scientific reports11:1537 2019 |
| PubMed ID: 33452395 |
| |
| Chan W, Lee M, Yeo ZX, Ying D, Grimaldi KA, Pickering C, Yang MMS, Sundaram SK, Tzang LCH, Development and validation of next generation sequencing based 35-gene hereditary cancer panel Hereditary cancer in clinical practice18:9 2019 |
| PubMed ID: 32368312 |
| |
| Chaubey A, Shenoy S, Mathur A, Ma Z, Valencia CA, Reddy Nallamilli BR, Szekeres E, Stansberry L, Liu R, Hegde MR, Low-Pass Genome Sequencing: Validation and Diagnostic Utility from 409 Clinical Cases of Low-Pass Genome Sequencing for the Detection of Copy Number Variants to Replace Constitutional Microarray The Journal of molecular diagnostics : JMD22:823-840 2019 |
| PubMed ID: 32344035 |
| |
| Chen J, Li X, Zhong H, Meng Y, Du H, Systematic comparison of germline variant calling pipelines cross multiple next-generation sequencers Scientific reports9:9345 2019 |
| PubMed ID: 31249349 |
| |
| Chen Z, Pham L, Wu TC, Mo G, Xia Y, Chang PL, Porter D, Phan T, Che H, Tran H, Bansal V, Shaffer J, Belda-Ferre P, Humphrey G, Knight R, Pevzner P, Pham S, Wang Y, Lei M, Ultra-low input single tube linked-read library method enables short-read second-generation sequencing systems to generate highly accurate and economical long-range sequencing information routinely Genome research9:9345 2019 |
| PubMed ID: 32540955 |
| |
| Di Genova A, Buena-Atienza E, Ossowski S, Sagot MF, Efficient hybrid de novo assembly of human genomes with WENGAN Nature biotechnology9:9345 2019 |
| PubMed ID: 33318652 |
| |
| Factor DC, Barbeau AM, Allan KC, Hu LR, Madhavan M, Hoang AT, Hazel KEA, Hall PA, Nisraiyya S, Najm FJ, Miller TE, Nevin ZS, Karl RT, Lima BR, Song Y, Sibert AG, Dhillon GK, Volsko C, Bartels CF, Adams DJ, Dutta R, Gallagher MD, Phu W, Kozlenkov A, Dracheva S, Scacheri PC, Tesar PJ, Corradin O, Cell Type-Specific Intralocus Interactions Reveal Oligodendrocyte Mechanisms in MS Cell181:382-395.e21 2019 |
| PubMed ID: 32246942 |
| |
| Fotsing SF, Margoliash J, Wang C, Saini S, Yanicky R, Shleizer-Burko S, Goren A, Gymrek M, The impact of short tandem repeat variation on gene expression Nature genetics181:382-395.e21 2019 |
| PubMed ID: 31676866 |
| |
| Fujiki R, Ikeda M, Ohara O, Short DNA Probes Developed for Sample Tracking and Quality Assurance in Gene Panel Testing The Journal of molecular diagnostics : JMD181:382-395.e21 2019 |
| PubMed ID: 31445212 |
| |
| Gaedigk A, Turner A, Everts RE, Scott SA, Aggarwal P, Broeckel U, McMillin GA, Melis R, Boone EC, Pratt VM, Kalman LV, Characterization of Reference Materials for Genetic Testing of CYP2D6 Alleles A GeT-RM Collaborative Project The Journal of molecular diagnostics : JMD181:382-395.e21 2019 |
| PubMed ID: 31401124 |
| |
| Gilpatrick T, Lee I, Graham JE, Raimondeau E, Bowen R, Heron A, Downs B, Sukumar S, Sedlazeck FJ, Timp W, Targeted nanopore sequencing with Cas9-guided adapter ligation Nature biotechnology181:382-395.e21 2019 |
| PubMed ID: 32042167 |
| |
| Guo R, Zhang Y, Teng M, Jiang C, Schineller M, Zhao B, Doench JG, O'Reilly RJ, Cesarman E, Giulino-Roth L, Gewurz BE, DNA methylation enzymes and PRC1 restrict B-cell Epstein-Barr virus oncoprotein expression Nature microbiology181:382-395.e21 2019 |
| PubMed ID: 32424339 |
| |
| Heft IE, Mostovoy Y, Levy-Sakin M, Ma W, Stevens AJ, Pastor S, McCaffrey J, Boffelli D, Martin DI, Xiao M, Kennedy MA, Kwok PY, Sikela JM, The Driver of Extreme Human-Specific Olduvai Repeat Expansion Remains Highly Active in the Human Genome Genetics181:382-395.e21 2019 |
| PubMed ID: 31754017 |
| |
| Hu J, Li W, Adebali O, Yang Y, Oztas O, Selby CP, Sancar A, Genome-wide mapping of nucleotide excision repair with XR-seq Nature Protocols14:248-282 2019 |
| PubMed ID: 30552409 |
| |
| Izevbaye I, Liang LY, Mather C, El-Hallani S, Maglantay R, Saini L, Clinical Validation of a Myeloid Next-Generations Sequencing Panel for Single Nucleotide Variants, Indels, and Fusion Genes The Journal of molecular diagnostics : JMD14:248-282 2019 |
| PubMed ID: 31751678 |
| |
| Jenkins MM, Almli LM, Pangilinan F, Chong JX, Blue EE, Shapira SK, White J, McGoldrick D, Smith JD, Mullikin JC, Bean CJ, Nembhard WN, Lou XY, Shaw GM, Romitti PA, Keppler-Noreuil K, Yazdy MM, Kay DM, Carter TC, Olshan AF, Moore KJ, Nascone-Yoder N, Finnell RH, Lupo PJ, Feldkamp ML, NISC Comparative Sequencing Program ML, University of Washington Center for Mendelian Genomics ML, Nickerson DA, Bamshad MJ, Brody LC, Reefhuis J, National Birth Defects Prevention Study J, Exome sequencing of family trios from the National Birth Defects Prevention Study: Tapping into a rich resource of genetic and environmental data Birth defects research14:248-282 2019 |
| PubMed ID: 31328417 |
| |
| Kader T, Elder K, Zethoven M, Semple T, Hill P, Goode DL, Thio N, Cheasley D, Rowley SM, Byrne DJ, Pang JM, Miligy IM, Green AR, Rakha EA, Fox SB, Mann GB, Campbell IG, Gorringe KL, The genetic architecture of breast papillary lesions as a predictor of progression to carcinoma NPJ breast cancer6:9 2019 |
| PubMed ID: 32195332 |
| |
| Kathuria K, Ratan A, SVXplorer: Three-tier approach to identification of structural variants via sequential recombination of discordant cluster signatures PLoS computational biology16:e1007737 2019 |
| PubMed ID: 32182236 |
| |
| Koboldt DC, Best practices for variant calling in clinical sequencing Genome medicine12:91 2019 |
| PubMed ID: 33106175 |
| |
| Lazzarotto CR, Malinin NL, Li Y, Zhang R, Yang Y, Lee G, Cowley E, He Y, Lan X, Jividen K, Katta V, Kolmakova NG, Petersen CT, Qi Q, Strelcov E, Maragh S, Krenciute G, Ma J, Cheng Y, Tsai SQ, CHANGE-seq reveals genetic and epigenetic effects on CRISPR-Cas9 genome-wide activity Nature biotechnology12:91 2019 |
| PubMed ID: 32541958 |
| |
| Lee J, Heo S, Bang D, Applying a Linear Amplification Strategy to Recombinase Polymerase Amplification for Uniform DNA Library Amplification ACS omega4:19953-19958 2019 |
| PubMed ID: 31788628 |
| |
| Leung ML, Watson DJ, Vaccaro CN, Mafra F, Wenocur A, Wang T, Hakonarson H, Santani A, Evaluating sequence data quality from the Swift Accel-Amplicon CFTR Panel Scientific data7:8 2019 |
| PubMed ID: 31913291 |
| |
| Liu C, Zhang Y, Li X, Jia Y, Li F, Li J, Zhang Z, Evidence of constraint in the 3D genome for trans-splicing in human cells Science China Life sciences7:8 2019 |
| PubMed ID: 32221814 |
| |
| Lu L, Liu X, Huang WK, Giusti-Rodríguez P, Cui J, Zhang S, Xu W, Wen Z, Ma S, Rosen JD, Xu Z, Bartels CF, Kawaguchi R, Hu M, Scacheri PC, Rong Z, Li Y, Sullivan PF, Song H, Ming GL, Li Y, Jin F, Robust Hi-C Maps of Enhancer-Promoter Interactions Reveal the Function of Non-coding Genome in Neural Development and Diseases Molecular cell7:8 2019 |
| PubMed ID: 32592681 |
| |
| Massey DJ, Kim D, Brooks KE, Smolka MB, Koren A, Next-Generation Sequencing Enables Spatiotemporal Resolution of Human Centromere Replication Timing Genes10:8 2019 |
| PubMed ID: 30987063 |
| |
| McCabe MJ, Gauthier MA, Chan CL, Thompson TJ, De Sousa SMC, Puttick C, Grady JP, Gayevskiy V, Tao J, Ying K, Cipponi A, Deng N, Swarbrick A, Thomas ML, Lord RV, Johns AL, Kohonen-Corish M, O'Toole SA, Clark J, Mueller SA, Gupta R, McCormack AI, Dinger ME, Cowley MJ, kConFab MJ, Development and validation of a targeted gene sequencing panel for application to disparate cancers Scientific reports9:17052 2019 |
| PubMed ID: 31745186 |
| |
| McClain L, Segreti AM, Nau S, Shaw P, Finegold DN, Pan LA, Peters DG, Chromosome 15q133 microduplications are associated with treatment refractory major depressive disorder Genes, brain, and behavior9:e12628 2019 |
| PubMed ID: 31828948 |
| |
| Miyao A, Kiyomiya JS, Iida K, Doi K, Yasue H, Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data BMC bioinformatics20:362 2019 |
| PubMed ID: 31253084 |
| |
| Orchard P, Kyono Y, Hensley J, Kitzman JO, Parker SCJ, Quantification, Dynamic Visualization, and Validation of Bias in ATAC-Seq Data with ataqv Cell systems10:298-306.e4 2019 |
| PubMed ID: 32213349 |
| |
| Osorio D, Yu X, Zhong Y, Li G, Yu P, Serpedin E, Huang JZ, Cai JJ, Single-Cell Expression Variability Implies Cell Function Cells9:298-306.e4 2019 |
| PubMed ID: 31861624 |
| |
| Quinodoz SA, Bhat P, Chovanec P, Jachowicz JW, Ollikainen N, Detmar E, Soehalim E, Guttman M, SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding Nature protocols17:36-75 2019 |
| PubMed ID: 35013617 |
| |
| Razavi P, Li BT, Brown DN, Jung B, Hubbell E, Shen R, Abida W, Juluru K, De Bruijn I, Hou C, Venn O, Lim R, Anand A, Maddala T, Gnerre S, Vijaya Satya R, Liu Q, Shen L, Eattock N, Yue J, Blocker AW, Lee M, Sehnert A, Xu H, Hall MP, Santiago-Zayas A, Novotny WF, Isbell JM, Rusch VW, Plitas G, Heerdt AS, Ladanyi M, Hyman DM, Jones DR, Morrow M, Riely GJ, Scher HI, Rudin CM, Robson ME, Diaz LA, Solit DB, Aravanis AM, Reis-Filho JS, High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants Nature medicine25:1928-1937 2019 |
| PubMed ID: 31768066 |
| |
| Rosenthal SH, Sun W, Zhang K, Liu Y, Nguyen Q, Gerasimova A, Nery C, Cheng L, Castonguay C, Hiller E, Li J, Elzinga C, Wolfson D, Smolgovsky A, Chen R, Buller-Burckle A, Catanese J, Grupe A, Lacbawan F, Owen R, Development and Validation of a 34-Gene Inherited Cancer Predisposition Panel Using Next-Generation Sequencing BioMed research international2020:3289023 2019 |
| PubMed ID: 32090079 |
| |
| Sangkuhl K, Whirl-Carrillo M, Whaley RM, Woon M, Lavertu A, Altman RB, Carter L, Verma A, Ritchie MD, Klein TE, Pharmacogenomics Clinical Annotation Tool (PharmCAT) Clinical pharmacology and therapeutics2020:3289023 2019 |
| PubMed ID: 31306493 |
| |
| Sarma M, Lee J, Ma S, Li S, Lu C, A diffusion-based microfluidic device for single-cell RNA-seq Lab on a chip2020:3289023 2019 |
| PubMed ID: 30815639 |
| |
| Shi X, Radhakrishnan S, Wen J, Chen JY, Chen J, Lam BA, Mills RE, Stranger BE, Lee C, Setlur SR, Association of CNVs with methylation variation NPJ genomic medicine5:41 2019 |
| PubMed ID: 33062306 |
| |
| Toss MS, Abidi A, Lesche D, Joseph C, Mahale S, Saunders H, Kader T, Miligy IM, Green AR, Gorringe KL, Rakha EA, The prognostic significance of immune microenvironment in breast ductal carcinoma in situ British journal of cancer5:41 2019 |
| PubMed ID: 32203210 |
| |
| Trzaskoma P, Ruszczycki B, Lee B, Pels KK, Krawczyk K, Bokota G, Szczepankiewicz AA, Aaron J, Walczak A, Sliwinska MA, Magalska A, Kadlof M, Wolny A, Parteka Z, Arabasz S, Kiss-Arabasz M, Plewczynski D, Ruan Y, Wilczynski GM, Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization Nature communications11:2120 2019 |
| PubMed ID: 32358536 |
| |
| Twesigomwe D, Wright GEB, Drögemöller BI, da Rocha J, Lombard Z, Hazelhurst S, A systematic comparison of pharmacogene star allele calling bioinformatics algorithms: a focus on NPJ genomic medicine5:30 2019 |
| PubMed ID: 32789024 |
| |
| Wang LW, Wang Z, Ersing I, Nobre L, Guo R, Jiang S, Trudeau S, Zhao B, Weekes MP, Gewurz BE, Epstein-Barr virus subverts mevalonate and fatty acid pathways to promote infected B-cell proliferation and survival PLoS pathogens15:e1008030 2019 |
| PubMed ID: 31518366 |
| |
| Yamaguchi I, Watanabe T, Ohara O, Hasegawa Y, PCR-free whole exome sequencing: Cost-effective and efficient in detecting rare mutations PloS one14:e0222562 2019 |
| PubMed ID: 31518370 |
| |
| Zhang R, Gao P, Ding J, Li Z, Li J, Assessment of significant procedures in multigene molecular detection for breast cancer in clinical laboratories: from variant detection to targeted therapy Breast cancer (Tokyo, Japan)14:e0222562 2019 |
| PubMed ID: 31388961 |
| |
| Zhou W, Emery SB, Flasch DA, Wang Y, Kwan KY, Kidd JM, Moran JV, Mills RE, Identification and characterization of occult human-specific LINE-1 insertions using long-read sequencing technology Nucleic acids research14:e0222562 2019 |
| PubMed ID: 31853540 |
| |
| Alpern D, Gardeux V, Russeil J, Mangeat B, Meireles-Filho ACA, Breysse R, Hacker D, Deplancke B, BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing Genome biology20:71 2018 |
| PubMed ID: 30999927 |
| |
| Andrew M. Gross PhD, Subramanian S. Ajay PhD, Vani Rajan MS, Carolyn Brown CGC, Krista Bluske PhD, Nicole J. Burns MS, Aditi Chawla PhD, Alison J. Coffey PhD, Alka Malhotra PhD, Alicia Scocchia MS CGC, Erin Thorpe MS CGC, Natasa Dzidic MS, Karine Hovanes PhD FACMG, Trilochan Sahoo MD FACMG, Egor Dolzhenko PhD, Bryan Lajoie PhD, Amirah Khouzam MS CGC, Shimul Chowdhury PhD FACMG, John Belmont MD PhD, Eric Roller PhD, Sergii Ivakhno PhD, Stephen Tanner PhD, Julia McEachern PA MHS, Tina Hambuch PhD FACMG, Michael Eberle PhD, R. Tanner Hagelstrom PhD FACMG, David R. Bentley PhD, Denise L. Perry MS CGC & Ryan J. Taft PhD, Copy-number variants in clinical genome sequencing: deployment and interpretation for rare and undiagnosed disease Genetics in Medicine20:71 2018 |
| PubMed ID: 30293986 |
| |
| Audano PA, Sulovari A, Graves-Lindsay TA, Cantsilieris S, Sorensen M, Welch AE, Dougherty ML, Nelson BJ, Shah A, Dutcher SK, Warren WC, Magrini V, McGrath SD, Li YI, Wilson RK, Eichler EE, Characterizing the Major Structural Variant Alleles of the Human Genome Cell176:663-675.e19 2018 |
| PubMed ID: 30661756 |
| |
| Balajee AS1, Sanders JT2, Golloshi R2, Shuryak I3, McCord RP2, Dainiak N, Investigation of Spatial Organization of Chromosome Territories in Chromosome Exchange Aberrations After Ionizing Radiation Exposure Health Physics115:77-89 2018 |
| PubMed ID: 29787433 |
| |
| Ben Aim L, Pigny P, Castro-Vega LJ, Buffet A, Amar L, Bertherat J, Drui D, Guilhem I, Baudin E, Lussey-Lepoutre C, Corsini C, Chabrier G, Briet C, Faivre L, Cardot-Bauters C, Favier J, Gimenez-Roqueplo AP, Burnichon N, Targeted next-generation sequencing detects rare genetic events in pheochromocytoma and paraganglioma Journal of medical genetics115:77-89 2018 |
| PubMed ID: 30877234 |
| |
| Blombery P, Jones K, Doig K, Ryland G, McBean M, Thompson E, Yannakou CK, Westerman D, Sensitive NPM1 Mutation Quantitation in Acute Myeloid Leukemia Using Ultradeep Next-Generation Sequencing in the Diagnostic Laboratory Archives of pathology & laboratory medicine115:77-89 2018 |
| PubMed ID: 29425073 |
| |
| Bowden R, Davies RW, Heger A, Pagnamenta AT, de Cesare M, Oikkonen LE, Parkes D, Freeman C, Dhalla F, Patel SY, Popitsch N, Ip CLC, Roberts HE, Salatino S, Lockstone H, Lunter G, Taylor JC, Buck D, Simpson MA, Donnelly P, Sequencing of human genomes with nanopore technology Nature communications10:1869 2018 |
| PubMed ID: 31015479 |
| |
| Brocard M, Khasnis S, Wood CD, Shannon-Lowe C, West MJ, Pumilio directs deadenylation-associated translational repression of the cyclin-dependent kinase 1 activator RGC-32 Nucleic acids research10:1869 2018 |
| PubMed ID: 29385536 |
| |
| Cameron DL, Di Stefano L, Papenfuss AT, Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software Nature communications10:3240 2018 |
| PubMed ID: 31324872 |
| |
| Cheasley D, Wakefield MJ, Ryland GL, Allan PE, Alsop K, Amarasinghe KC, Ananda S, Anglesio MS, Au-Yeung G, Böhm M, Bowtell DDL, Brand A, Chenevix-Trench G, Christie M, Chiew YE, Churchman M, DeFazio A, Demeo R, Dudley R, Fairweather N, Fedele CG, Fereday S, Fox SB, Gilks CB, Gourley C, Hacker NF, Hadley AM, Hendley J, Ho GY, Hughes S, Hunstman DG, Hunter SM, Jobling TW, Kalli KR, Kaufmann SH, Kennedy CJ, Köbel M, Le Page C, Li J, Lupat R, McNally OM, McAlpine JN, Mes-Masson AM, Mileshkin L, Provencher DM, Pyman J, Rahimi K, Rowley SM, Salazar C, Samimi G, Saunders H, Semple T, Sharma R, Sharpe AJ, Stephens AN, Thio N, Torres MC, Traficante N, Xing Z, Zethoven M, Antill YC, Scott CL, Campbell IG, Gorringe KL, The molecular origin and taxonomy of mucinous ovarian carcinoma Nature communications10:3935 2018 |
| PubMed ID: 31477716 |
| |
| Cleveland MH1, Zook JM2, Salit M3, Vallone PM2., Determining Performance Metrics for Targeted Next-Generation Sequencing Panels Using Reference Materials Journal of Molecular Diagnostics18:1525-1578 2018 |
| PubMed ID: 29959024 |
| |
| Giner-Delgado C, Villatoro S, Lerga-Jaso J, Gayà-Vidal M, Oliva M, Castellano D, Pantano L, Bitarello BD, Izquierdo D, Noguera I, Olalde I, Delprat A, Blancher A, Lalueza-Fox C, Esko T, O'Reilly PF, Andrés AM, Ferretti L, Puig M, Cáceres M, Evolutionary and functional impact of common polymorphic inversions in the human genome Nature communications10:4222 2018 |
| PubMed ID: 31530810 |
| |
| Harwood JC, Kent NA, Allen ND, Harwood AJ, Nucleosome dynamics of human iPSC during neural differentiation EMBO reports20:4222 2018 |
| PubMed ID: 31036712 |
| |
| Heyer EE, Deveson IW, Wooi D, Selinger CI, Lyons RJ, Hayes VM, O'Toole SA, Ballinger ML, Gill D, Thomas DM, Mercer TR, Blackburn J, Diagnosis of fusion genes using targeted RNA sequencing Nature communications10:1388 2018 |
| PubMed ID: 30918253 |
| |
| Hwang KB, Lee IH, Li H, Won DG, Hernandez-Ferrer C, Negron JA, Kong SW, Comparative analysis of whole-genome sequencing pipelines to minimize false negative findings Scientific reports9:3219 2018 |
| PubMed ID: 30824715 |
| |
| Johnston AD, Simões-Pires CA, Thompson TV, Suzuki M, Greally JM, Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding Nature communications10:3472 2018 |
| PubMed ID: 31375681 |
| |
| Kajitani R, Yoshimura D, Okuno M, Minakuchi Y, Kagoshima H, Fujiyama A, Kubokawa K, Kohara Y, Toyoda A, Itoh T, Platanus-allee is a de novo haplotype assembler enabling a comprehensive access to divergent heterozygous regions Nature communications10:1702 2018 |
| PubMed ID: 30979905 |
| |
| Kim D, Paggi JM, Park C, Bennett C, Salzberg SL, Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype Nature biotechnology37:907-915 2018 |
| PubMed ID: 31375807 |
| |
| Lazzarotto CR1, Nguyen NT2,3, Tang X1, Malagon-Lopez J2,4,5, Guo JA2, Aryee MJ2,4,5, Joung JK2,4, Tsai SQ6., Defining CRISPR-Cas9 genome-wide nuclease activities with CIRCLE-seq Nat Protoc13:2615-2642 2018 |
| PubMed ID: 30341435 |
| |
| Lee DS, Luo C, Zhou J, Chandran S, Rivkin A, Bartlett A, Nery JR, Fitzpatrick C, O'Connor C, Dixon JR, Ecker JR, Simultaneous profiling of 3D genome structure and DNA methylation in single human cells Nature methods13:2615-2642 2018 |
| PubMed ID: 31501549 |
| |
| Lee J, Lim H, Jang H, Hwang B, Lee JH, Cho J, Lee JH, Bang D, CRISPR-Cap: multiplexed double-stranded DNA enrichment based on the CRISPR system Nucleic acids research13:2615-2642 2018 |
| PubMed ID: 30215766 |
| |
| Lincoln SE, Truty R, Lin CF, Zook JM, Paul J, Ramey VH, Salit M, Rehm HL, Nussbaum RL, Lebo MS, A Rigorous Interlaboratory Examination of the Need to Confirm Next-Generation Sequencing-Detected Variants with an Orthogonal Method in Clinical Genetic Testing The Journal of molecular diagnostics : JMD13:2615-2642 2018 |
| PubMed ID: 30610921 |
| |
| Ma ZS, Li L, Ye C, Peng M, Zhang YP, Hybrid assembly of ultra-long Nanopore reads augmented with 10x-Genomics contigs: Demonstrated with a human genome Genomics13:2615-2642 2018 |
| PubMed ID: 30594583 |
| |
| Maggiolini FAM, Cantsilieris S, D'Addabbo P, Manganelli M, Coe BP, Dumont BL, Sanders AD, Pang AWC, Vollger MR, Palumbo O, Palumbo P, Accadia M, Carella M, Eichler EE, Antonacci F, Genomic inversions and GOLGA core duplicons underlie disease instability at the 15q25 locus PLoS genetics15:e1008075 2018 |
| PubMed ID: 30917130 |
| |
| Michael J. Keogh, Wei Wei, Juvid Aryaman, Lauren Walker, Jelle van den Ameele, Jon Coxhead, Ian Wilson, Matthew Bashton, Jon Beck, John West, Richard Chen, Christian Haudenschild, Gabor Bartha, Shujun Luo, Chris M. Morris, Nick S. Jones, Johannes Attems & Patrick F. Chinnery, High prevalence of focal and multi-focal somatic genetic variants in the human brain Nature Communications9:4257 2018 |
| PubMed ID: 30323172 |
| |
| Mitsuhashi S, Frith MC, Mizuguchi T, Miyatake S, Toyota T, Adachi H, Oma Y, Kino Y, Mitsuhashi H, Matsumoto N, Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads Genome biology20:58 2018 |
| PubMed ID: 30890163 |
| |
| Mumbach MR, Granja JM, Flynn RA, Roake CM, Satpathy AT, Rubin AJ, Qi Y, Jiang Z, Shams S, Louie BH, Guo JK, Gennert DG, Corces MR, Khavari PA, Atianand MK, Artandi SE, Fitzgerald KA, Greenleaf WJ, Chang HY, HiChIRP reveals RNA-associated chromosome conformation Nature methods16:489-492 2018 |
| PubMed ID: 31133759 |
| |
| Peng Q, Xu C, Kim D, Lewis M, DiCarlo J, Wang Y, Targeted Single Primer Enrichment Sequencing with Single End Duplex-UMI Scientific reports9:4810 2018 |
| PubMed ID: 30886209 |
| |
| Pliner HA1, Packer JS1, McFaline-Figueroa JL1, Cusanovich DA1, Daza RM1, Aghamirzaie D1, Srivatsan S1, Qiu X2, Jackson D1, Minkina A1, Adey AC3, Steemers FJ4, Shendure J5, Trapnell C6., Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data Molecular Cell9:4810 2018 |
| PubMed ID: 30078726 |
| |
| Quinodoz SA1, Ollikainen N1, Tabak B2, Palla A1, Schmidt JM1, Detmar E1, Lai MM1, Shishkin AA1, Bhat P3, Takei Y1, Trinh V1, Aznauryan E1, Russell P4, Cheng C5, Jovanovic M6, Chow A1, Cai L1, McDonel P2, Garber M2, Guttman M, Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus Cell174:744-757 2018 |
| PubMed ID: 29887377 |
| |
| Stephen Bruinsma, Joshua Burgess, Daniel Schlingman, Agata Czyz, Natalie Morrell, Catherine Ballenger, Heather Meinholz, Lee Brady, Anupama Khanna, Lindsay Freeberg, Rosamond G Jackson, Pascale Mathonet, Susan C Verity, Andrew F Slatter, Rooz Golshani, Haiying Grunenwald, Gary P Schroth and Niall A Gormley, Bead-linked transposomes enable a normalization-free workflow for NGS library preparation BMC Genomics19:722 2018 |
| PubMed ID: 30285621 |
| |
| Surrey LF, MacFarland SP, Chang F, Cao K, Rathi KS, Akgumus GT, Gallo D, Lin F, Gleason A, Raman P, Aplenc R, Bagatell R, Minturn J, Mosse Y, Santi M, Tasian SK, Waanders AJ, Sarmady M, Maris JM, Hunger SP, Li MM, Clinical utility of custom-designed NGS panel testing in pediatric tumors Genome medicine11:32 2018 |
| PubMed ID: 31133068 |
| |
| Swart M, Stansberry WM, Pratt VM, Medeiros EB, Kiel PJ, Shen F, Schneider BP, Skaar TC, Analytical Validation of Variants to Aid in Genotype-Guided Therapy for Oncology The Journal of molecular diagnostics : JMD21:491-502 2018 |
| PubMed ID: 30794985 |
| |
| Velasco G, Grillo G, Touleimat N, Ferry L, Ivkovic I, Ribierre F, Deleuze JF, Chantalat S, Picard C, Francastel C, Comparative methylome analysis of ICF patients identifies heterochromatin loci that require ZBTB24, CDCA7 and HELLS for their methylated state Human molecular genetics21:491-502 2018 |
| PubMed ID: 29659838 |
| |
| Wang LW, Shen H, Nobre L, Ersing I, Paulo JA, Trudeau S, Wang Z, Smith NA, Ma Y, Reinstadler B, Nomburg J, Sommermann T, Cahir-McFarland E, Gygi SP, Mootha VK, Weekes MP, Gewurz BE, Epstein-Barr-Virus-Induced One-Carbon Metabolism Drives B Cell Transformation Cell metabolism21:491-502 2018 |
| PubMed ID: 31257153 |
| |
| Wang X, He L, Goggin SM, Saadat A, Wang L, Sinnott-Armstrong N, Claussnitzer M, Kellis M, High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human Nature Communications9:491-502 2018 |
| PubMed ID: 30568279 |
| |
| Yeeok Kang, Seong-Hyeuk Nam, Kyung Sun Park, Yoonjung Kim, Jong-Won Kim, Eunjung Lee, Jung Min Ko, Kyung-A Lee and Inho ParkEmail, DeviCNV: detection and visualization of exon-level copy number variants in targeted next-generation sequencing data BMC Bioinformatics19:491-502 2018 |
| PubMed ID: 30326846 |
| |
| Zhang M, Ngampeerapong C, Redin D, Ahmadian A, Sychugov I, Linnros J, Thermophoresis-Controlled Size-Dependent DNA Translocation through an Array of Nanopores ACS nano12:4574-4582 2018 |
| PubMed ID: 29648793 |
| |
| Zhu B, Hsieh YP, Murphy TW, Zhang Q, Naler LB, Lu C, MOWChIP-seq for low-input and multiplexed profiling of genome-wide histone modifications Nature protocols12:4574-4582 2018 |
| PubMed ID: 31666743 |
| |
| Becker T, Lee WP, Leone J, Zhu Q, Zhang C, Liu S, Sargent J, Shanker K, Mil-Homens A, Cerveira E, Ryan M, Cha J, Navarro FCP, Galeev T, Gerstein M, Mills RE, Shin DG, Lee C, Malhotra A, FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods Genome biology19:38 2017 |
| PubMed ID: 29559002 |
| |
| Blackburn J, Wong T, Madala BS, Barker C, Hardwick SA, Reis ALM, Deveson IW, Mercer TR, Use of synthetic DNA spike-in controls (sequins) for human genome sequencing Nature protocols14:2119-2151 2017 |
| PubMed ID: 31217595 |
| |
| Doig KD, Ellul J, Fellowes A, Thompson ER, Ryland G, Blombery P, Papenfuss AT, Fox SB, Canary: an atomic pipeline for clinical amplicon assays BMC bioinformatics18:555 2017 |
| PubMed ID: 29246107 |
| |
| Garieri M1,2,3, Delaneau O1,2,3, Santoni F1,4, Fish RJ1, Mull D1, Carninci P5, Dermitzakis ET1,2,3, Antonarakis SE1,2,4, Fort A6., The effect of genetic variation on promoter usage and enhancer activity. Nat Commun8(1):1358 2017 |
| PubMed ID: 29116076 |
| |
| Kamps-Hughes N, McUsic A, Kurihara L, Harkins TT, Pal P, Ray C, Ionescu-Zanetti C, ERASE-Seq: Leveraging replicate measurements to enhance ultralow frequency variant detection in NGS data PloS one13:e0195272 2017 |
| PubMed ID: 29630678 |
| |
| Lee JEA, Li N, Rowley SM, Cheasley D, Zethoven M, McInerny S, Gorringe KL, James PA, Campbell IG, Molecular analysis of PALB2 associated breast cancers The Journal of pathology13:e0195272 2017 |
| PubMed ID: 29431189 |
| |
| Liu Y, Cao Z, Wang Y, Guo Y, Xu P, Yuan P, Liu Z, He Y, Wei W, Genome-wide screening for functional long noncoding RNAs in human cells by Cas9 targeting of splice sites Nature biotechnology13:e0195272 2017 |
| PubMed ID: 30395134 |
| |
| Mulqueen RM, Pokholok D, Norberg SJ, Torkenczy KA, Fields AJ, Sun D, Sinnamon JR, Shendure J, Trapnell C, O'Roak BJ, Xia Z, Steemers FJ, Adey AC, Highly scalable generation of DNA methylation profiles in single cells Nature biotechnology36:428-431 2017 |
| PubMed ID: 29644997 |
| |
| Numanagic I, Malikic S, Ford M, Qin X, Toji L, Radovich M, Skaar TC, Pratt VM, Berger B, Scherer S, Sahinalp SC, Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes Nature communications9:828 2017 |
| PubMed ID: 29483503 |
| |
| Preissl S, Fang R, Huang H, Zhao Y, Raviram R, Gorkin DU, Zhang Y, Sos BC, Afzal V, Dickel DE, Kuan S, Visel A, Pennacchio LA, Zhang K, Ren B, Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation Nature neuroscience21:432-439 2017 |
| PubMed ID: 29434377 |
| |
| Shigemizu D, Miya F, Akiyama S, Okuda S, Boroevich KA, Fujimoto A, Nakagawa H, Ozaki K, Niida S, Kanemura Y, Okamoto N, Saitoh S, Kato M, Yamasaki M, Matsunaga T, Mutai H, Kosaki K, Tsunoda T, IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis Scientific reports8:5608 2017 |
| PubMed ID: 29618752 |
| |
| Soukupova J, Zemankova P, Lhotova K, Janatova M, Borecka M, Stolarova L, Lhota F, Foretova L, Machackova E, Stranecky V, Tavandzis S, Kleiblova P, Vocka M, Hartmannova H, Hodanova K, Kmoch S, Kleibl Z, Validation of CZECANCA (CZEch CAncer paNel for Clinical Application) for targeted NGS-based analysis of hereditary cancer syndromes PloS one13:e0195761 2017 |
| PubMed ID: 29649263 |
| |
| Trost B, Walker S, Wang Z, Thiruvahindrapuram B, MacDonald JR, Sung WWL, Pereira SL, Whitney J, Chan AJS, Pellecchia G, Reuter MS, Lok S, Yuen RKC, Marshall CR, Merico D, Scherer SW, A Comprehensive Workflow for Read Depth-Based Identification of Copy-Number Variation from Whole-Genome Sequence Data American journal of human genetics102:142-155 2017 |
| PubMed ID: 29304372 |
| |
| Pratt VM, Everts RE, Aggarwal P, Beyer BN, Broeckel U, Epstein-Baak R, Hujsak P, Kornreich R, Liao J, Lorier R, Scott SA, Smith CH, Toji LH, Turner A, Kalman LV., A Comprehensive Workflow for Read Depth-Based Identification of Copy-Number Variation from Whole-Genome Sequence Data Characterization of 137 Genomic DNA Reference Materials for 28 Pharmacogenetic Genes: A GeT-RM Collaborative Project.18(1):109-23 2016 |
| PubMed ID: 26621101 |
| |
| Chennagiri N, White EJ, Frieden A, Lopez E, Lieber DS, Nikiforov A, Ross T, Batorsky R, Hansen S, Lip V, Luquette LJ, Mauceli E, Margulies D, Milos PM, Napolitano N, Nizzari MM, Yu T, Thompson JF, Orthogonal NGS for High Throughput Clinical Diagnostics Scientific reports6:24650 2015 |
| PubMed ID: 27090146 |
| |
| Core LJ, Martins AL, Danko CG, Waters CT, Siepel A, Lis JT, Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers Nature genetics46:1311-20 2014 |
| PubMed ID: 25383968 |
| |
| Zook JM, Chapman B, Wang J, Mittelman D, Hofmann O, Hide W, Salit M., Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat Biotechnol.32(3):246-51 2014 |
| PubMed ID: 24531798 |
| |
| Dames S, Chou LS, Xiao Y, Wayman T, Stocks J, Singleton M, Eilbeck K, Mao R, The Development of Next-Generation Sequencing Assays for the Mitochondrial Genome and 108 Nuclear Genes Associated with Mitochondrial Disorders The Journal of molecular diagnostics : JMD32(3):246-51 2013 |
| PubMed ID: 23665194 |
| |
| Carneiro MO, Russ C, Ross MG, Gabriel SB, Nusbaum C, DePristo MA, Pacific biosciences sequencing technology for genotyping and variation discovery in human data BMC genomics13:375 2012 |
| PubMed ID: 22863213 |
| |
| Girirajan S, Dennis MY, Baker C, Malig M, Coe BP, Campbell CD, Mark K, Vu TH, Alkan C, Cheng Z, Biesecker LG, Bernier R, Eichler EE, Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder American journal of human genetics92:221-37 2012 |
| PubMed ID: 23375656 |
| |
| Liang WS, Craig DW, Carpten J, Borad MJ, Demeure MJ, Weiss GJ, Izatt T, Sinari S, Christoforides A, Aldrich J, Kurdoglu A, Barrett M, Phillips L, Benson H, Tembe W, Braggio E, Kiefer JA, Legendre C, Posner R, Hostetter GH, Baker A, Egan JB, Han H, Lake D, Stites EC, Ramanathan RK, Fonseca R, Stewart AK, Von Hoff D, Genome-wide characterization of pancreatic adenocarcinoma patients using next generation sequencing PloS one7:e43192 2012 |
| PubMed ID: 23071490 |
| |
| Peters BA1, Kermani BG, Sparks AB, Alferov O, Hong P, Alexeev A, Jiang Y, Dahl F, Tang YT, Haas J, Robasky K, Zaranek AW, Lee JH, Ball MP, Peterson JE, Perazich H, Yeung G, Liu J, Chen L, Kennemer MI, Pothuraju K, Konvicka K, Tsoupko-Sitnikov M, Pant KP, Ebert JC, Nilsen GB, Baccash J, Halpern AL, Church GM, Drmanac R., Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Nature487(7406):190-5 2012 |
| PubMed ID: 22785314 |
| |
| Dennis MY, Nuttle X, Sudmant PH, Antonacci F, Graves TA, Nefedov M, Rosenfeld JA, Sajjadian S, Malig M, Kotkiewicz H, Curry CJ, Shafer S, Shaffer LG, de Jong PJ, Wilson RK, Eichler EE, Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication Cell149:912-22 2011 |
| PubMed ID: 22559943 |
| |
| ENCODE Project Consortium , Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, Epstein CB, Frietze S, Harrow J, Kaul R, Khatun J, Lajoie BR, Landt SG, Lee BK, Pauli F, Rosenbloom KR, Sabo P, Safi A, Sanyal A, Shoresh N, Simon JM, Song L, Trinklein ND, Altshuler RC, Birney E, Brown JB, Cheng C, Djebali S, Dong X, Dunham I, Ernst J, Furey TS, Gerstein M, Giardine B, Greven M, Hardison RC, Harris RS, Herrero J, Hoffman MM, Iyer S, Kelllis M, Khatun J, Kheradpour P, Kundaje A, Lassman T, Li Q, Lin X, Marinov GK, Merkel A, Mortazavi A, Parker SC, Reddy TE, Rozowsky J, Schlesinger F, Thurman RE, Wang J, Ward LD, Whitfield TW, Wilder SP, Wu W, Xi HS, Yip KY, Zhuang J, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M, Pazin MJ, Lowdon RF, Dillon LA, Adams LB, Kelly CJ, Zhang J, Wexler JR, Green ED, Good PJ, Feingold EA, Bernstein BE, Birney E, Crawford GE, Dekker J, Elinitski L, Farnham PJ, Gerstein M, Giddings MC, Gingeras TR, Green ED, Guigó R, Hardison RC, Hubbard TJ, Kellis M, Kent WJ, Lieb JD, Margulies EH, Myers RM, Snyder M, Starnatoyannopoulos JA, Tennebaum SA, Weng Z, White KP, Wold B, Khatun J, Yu Y, Wrobel J, Risk BA, Gunawardena HP, Kuiper HC, Maier CW, Xie L, Chen X, Giddings MC, Bernstein BE, Epstein CB, Shoresh N, Ernst J, Kheradpour P, Mikkelsen TS, Gillespie S, Goren A, Ram O, Zhang X, Wang L, Issner R, Coyne MJ, Durham T, Ku M, Truong T, Ward LD, Altshuler RC, Eaton ML, Kellis M, Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Batut P, Bell I, Bell K, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena HP, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Li G, Luo OJ, Park E, Preall JB, Presaud K, Ribeca P, Risk BA, Robyr D, Ruan X, Sammeth M, Sandu KS, Schaeffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Hayashizaki Y, Harrow J, Gerstein M, Hubbard TJ, Reymond A, Antonarakis SE, Hannon GJ, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR, Rosenbloom KR, Sloan CA, Learned K, Malladi VS, Wong MC, Barber GP, Cline MS, Dreszer TR, Heitner SG, Karolchik D, Kent WJ, Kirkup VM, Meyer LR, Long JC, Maddren M, Raney BJ, Furey TS, Song L, Grasfeder LL, Giresi PG, Lee BK, Battenhouse A, Sheffield NC, Simon JM, Showers KA, Safi A, London D, Bhinge AA, Shestak C, Schaner MR, Kim SK, Zhang ZZ, Mieczkowski PA, Mieczkowska JO, Liu Z, McDaniell RM, Ni Y, Rashid NU, Kim MJ, Adar S, Zhang Z, Wang T, Winter D, Keefe D, Birney E, Iyer VR, Lieb JD, Crawford GE, Li G, Sandhu KS, Zheng M, Wang P, Luo OJ, Shahab A, Fullwood MJ, Ruan X, Ruan Y, Myers RM, Pauli F, Williams BA, Gertz J, Marinov GK, Reddy TE, Vielmetter J, Partridge EC, Trout D, Varley KE, Gasper C, Bansal A, Pepke S, Jain P, Amrhein H, Bowling KM, Anaya M, Cross MK, King B, Muratet MA, Antoshechkin I, Newberry KM, McCue K, Nesmith AS, Fisher-Aylor KI, Pusey B, DeSalvo G, Parker SL, Balasubramanian S, Davis NS, Meadows SK, Eggleston T, Gunter C, Newberry JS, Levy SE, Absher DM, Mortazavi A, Wong WH, Wold B, Blow MJ, Visel A, Pennachio LA, Elnitski L, Margulies EH, Parker SC, Petrykowska HM, Abyzov A, Aken B, Barrell D, Barson G, Berry A, Bignell A, Boychenko V, Bussotti G, Chrast J, Davidson C, Derrien T, Despacio-Reyes G, Diekhans M, Ezkurdia I, Frankish A, Gilbert J, Gonzalez JM, Griffiths E, Harte R, Hendrix DA, Howald C, Hunt T, Jungreis I, Kay M, Khurana E, Kokocinski F, Leng J, Lin MF, Loveland J, Lu Z, Manthravadi D, Mariotti M, Mudge J, Mukherjee G, Notredame C, Pei B, Rodriguez JM, Saunders G, Sboner A, Searle S, Sisu C, Snow C, Steward C, Tanzer A, Tapanan E, Tress ML, van Baren MJ, Walters N, Washieti S, Wilming L, Zadissa A, Zhengdong Z, Brent M, Haussler D, Kellis M, Valencia A, Gerstein M, Raymond A, Guigó R, Harrow J, Hubbard TJ, Landt SG, Frietze S, Abyzov A, Addleman N, Alexander RP, Auerbach RK, Balasubramanian S, Bettinger K, Bhardwaj N, Boyle AP, Cao AR, Cayting P, Charos A, Cheng Y, Cheng C, Eastman C, Euskirchen G, Fleming JD, Grubert F, Habegger L, Hariharan M, Harmanci A, Iyenger S, Jin VX, Karczewski KJ, Kasowski M, Lacroute P, Lam H, Larnarre-Vincent N, Leng J, Lian J, Lindahl-Allen M, Min R, Miotto B, Monahan H, Moqtaderi Z, Mu XJ, O'Geen H, Ouyang Z, Patacsil D, Pei B, Raha D, Ramirez L, Reed B, Rozowsky J, Sboner A, Shi M, Sisu C, Slifer T, Witt H, Wu L, Xu X, Yan KK, Yang X, Yip KY, Zhang Z, Struhl K, Weissman SM, Gerstein M, Farnham PJ, Snyder M, Tenebaum SA, Penalva LO, Doyle F, Karmakar S, Landt SG, Bhanvadia RR, Choudhury A, Domanus M, Ma L, Moran J, Patacsil D, Slifer T, Victorsen A, Yang X, Snyder M, White KP, Auer T, Centarin L, Eichenlaub M, Gruhl F, Heerman S, Hoeckendorf B, Inoue D, Kellner T, Kirchmaier S, Mueller C, Reinhardt R, Schertel L, Schneider S, Sinn R, Wittbrodt B, Wittbrodt J, Weng Z, Whitfield TW, Wang J, Collins PJ, Aldred SF, Trinklein ND, Partridge EC, Myers RM, Dekker J, Jain G, Lajoie BR, Sanyal A, Balasundaram G, Bates DL, Byron R, Canfield TK, Diegel MJ, Dunn D, Ebersol AK, Ebersol AK, Frum T, Garg K, Gist E, Hansen RS, Boatman L, Haugen E, Humbert R, Jain G, Johnson AK, Johnson EM, Kutyavin TM, Lajoie BR, Lee K, Lotakis D, Maurano MT, Neph SJ, Neri FV, Nguyen ED, Qu H, Reynolds AP, Roach V, Rynes E, Sabo P, Sanchez ME, Sandstrom RS, Sanyal A, Shafer AO, Stergachis AB, Thomas S, Thurman RE, Vernot B, Vierstra J, Vong S, Wang H, Weaver MA, Yan Y, Zhang M, Akey JA, Bender M, Dorschner MO, Groudine M, MacCoss MJ, Navas P, Stamatoyannopoulos G, Kaul R, Dekker J, Stamatoyannopoulos JA, Dunham I, Beal K, Brazma A, Flicek P, Herrero J, Johnson N, Keefe D, Lukk M, Luscombe NM, Sobral D, Vaquerizas JM, Wilder SP, Batzoglou S, Sidow A, Hussami N, Kyriazopoulou-Panagiotopoulou S, Libbrecht MW, Schaub MA, Kundaje A, Hardison RC, Miller W, Giardine B, Harris RS, Wu W, Bickel PJ, Banfai B, Boley NP, Brown JB, Huang H, Li Q, Li JJ, Noble WS, Bilmes JA, Buske OJ, Hoffman MM, Sahu AO, Kharchenko PV, Park PJ, Baker D, Taylor J, Weng Z, Iyer S, Dong X, Greven M, Lin X, Wang J, Xi HS, Zhuang J, Gerstein M, Alexander RP, Balasubramanian S, Cheng C, Harmanci A, Lochovsky L, Min R, Mu XJ, Rozowsky J, Yan KK, Yip KY, Birney E, An integrated encyclopedia of DNA elements in the human genome Nature489:57-74 2011 |
| PubMed ID: 22955616 |
| |
| Shen P, Wang W, Krishnakumar S, Palm C, Chi AK, Enns GM, Davis RW, Speed TP, Mindrinos MN, Scharfe C, High-quality DNA sequence capture of 524 disease candidate genes Proceedings of the National Academy of Sciences of the United States of America108:6549-54 2011 |
| PubMed ID: 21467225 |
| |
| Aird D, Ross MG, Chen WS, Danielsson M, Fennell T, Russ C, Jaffe DB, Nusbaum C, Gnirke A, Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries Genome biology12:R18 2010 |
| PubMed ID: 21338519 |
| |
| Beck CR, Collier P, Macfarlane C, Malig M, Kidd JM, Eichler EE, Badge RM, Moran JV, LINE-1 retrotransposition activity in human genomes Cell141:1159-70 2010 |
| PubMed ID: 20602998 |
| |
| Campbell CD, Sampas N, Tsalenko A, Sudmant PH, Kidd JM, Malig M, Vu TH, Vives L, Tsang P, Bruhn L, Eichler EE, Population-genetic properties of differentiated human copy-number polymorphisms American journal of human genetics88:317-32 2010 |
| PubMed ID: 21397061 |
| |
| Ewing AD, Kazazian HH, High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes Genome research20:1262-70 2010 |
| PubMed ID: 20488934 |
| |
| Fisher S, Barry A, Abreu J, Minie B, Nolan J, Delorey TM, Young G, Fennell TJ, Allen A, Ambrogio L, Berlin AM, Blumenstiel B, Cibulskis K, Friedrich D, Johnson R, Juhn F, Reilly B, Shammas R, Stalker J, Sykes SM, Thompson J, Walsh J, Zimmer A, Zwirko Z, Gabriel S, Nicol R, Nusbaum C, A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries Genome biology12:R1 2010 |
| PubMed ID: 21205303 |
| |
| Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, Berlin AM, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, Jaffe DB, High-quality draft assemblies of mammalian genomes from massively parallel sequence data Proceedings of the National Academy of Sciences of the United States of America108:1513-8 2010 |
| PubMed ID: 21187386 |
| |
| McDaniell R, Lee BK, Song L, Liu Z, Boyle AP, Erdos MR, Scott LJ, Morken MA, Kucera KS, Battenhouse A, Keefe D, Collins FS, Willard HF, Lieb JD, Furey TS, Crawford GE, Iyer VR, Birney E, Heritable individual-specific and allele-specific chromatin signatures in humans Science (New York, NY)328:235-9 2010 |
| PubMed ID: 20299549 |
| |
| Stewart C, Kural D, Strömberg MP, Walker JA, Konkel MK, Stütz AM, Urban AE, Grubert F, Lam HY, Lee WP, Busby M, Indap AR, Garrison E, Huff C, Xing J, Snyder MP, Jorde LB, Batzer MA, Korbel JO, Marth GT, 1000 Genomes Project GT, A comprehensive map of mobile element insertion polymorphisms in humans PLoS genetics7:e1002236 2010 |
| PubMed ID: 21876680 |
| |
| Antonacci F, Kidd JM, Marques-Bonet T, Ventura M, Siswara P, Jiang Z, Eichler EE, Characterization of six human disease-associated inversion polymorphisms Human molecular genetics7:e1002236 2009 |
| PubMed ID: 19383631 |
| |
| Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, Shaffer T, Wong M, Bhattacharjee A, Eichler EE, Bamshad M, Nickerson DA, and Shendure J.
, Targeted capture and massively parallel sequencing of twelve human exomes Nature461(7261):272-276 2009 |
| PubMed ID: 19684571 |
| |
| Park H, Kim JI, Ju YS, Gokcumen O, Mills RE, Kim S, Lee S, Suh D, Hong D, Kang HP, Yoo YJ, Shin JY, Kim HJ, Yavartanoo M, Chang YW, Ha JS, Chong W, Hwang GR, Darvishi K, Kim H, Yang SJ, Yang KS, Kim H, Hurles ME, Scherer SW, Carter NP, Tyler-Smith C, Lee C, Seo JS, Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing Nature genetics42:400-5 2009 |
| PubMed ID: 20364138 |
| |
| Xue Y, Zhang X, Huang N, Daly A, Gillson CJ, Macarthur DG, Yngvadottir B, Nica AC, Woodwark C, Chen Y, Conrad DF, Ayub Q, Mehdi SQ, Li P, Tyler-Smith C, Population differentiation as an indicator of recent positive selection in humans: an empirical evaluation Genetics183:1065-77 2009 |
| PubMed ID: 19737746 |
| |
| Riethman H, Human subtelomeric copy number variations Cytogenetic and genome research123:244-52 2008 |
| PubMed ID: 19287161 |
| |
| Bovee D, Zhou Y, Haugen E, Wu Z, Hayden HS, Gillett W, Tuzun E, Cooper GM, Sampas N, Phelps K, Levy R, Morrison VA, Sprague J, Jewett D, Buckley D, Subramaniam S, Chang J, Smith DR, Olson MV, Eichler EE, Kaul R, Closing gaps in the human genome with fosmid resources generated from multiple individuals Nature genetics40:96-101 2007 |
| PubMed ID: 18157130 |
| |
| Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F, Haugen E, Zerr T, Yamada NA, Tsang P, Newman TL, Tüzün E, Cheng Z, Ebling HM, Tusneem N, David R, Gillett W, Phelps KA, Weaver M, Saranga D, Brand A, Tao W, Gustafson E, McKernan K, Chen L, Malig M, Smith JD, Korn JM, McCarroll SA, Altshuler DA, Peiffer DA, Dorschner M, Stamatoyannopoulos J, Schwartz D, Nickerson DA, Mullikin JC, Wilson RK, Bruhn L, Olson MV, Kaul R, Smith DR, Eichler EE, Mapping and sequencing of structural variation from eight human genomes Nature453:56-64 2007 |
| PubMed ID: 18451855 |
| |
| Podder M, Ruan J, Tripp W, Chu E, Tebbutt J, Robust SNP genotyping by multiplex PCR and arrayed primer extension BMC medical genomics1:5 2007 |
| PubMed ID: 18237385 |
| |
| de Bakker PI, McVean G, Sabeti PC, Miretti MM, Green T, Marchini J, Ke X, Monsuur AJ, Whittaker P, Delgado M, Morrison J, Richardson A, Walsh EC, Gao X, Galver L, Hart J, Hafler DA, Pericak-Vance M, Todd JA, Daly MJ, Trowsdale J, Wijmenga C, Vyse TJ, Beck S, Murray SS, Carrington M, Gregory S, Deloukas P, Rioux JD, A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC Nature Genetics38(10):1166-1172 2006 |
| PubMed ID: 16998491 |
| |
| Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, González JR, Gratacòs M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal T, Zhang J, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW, Hurles ME, Global variation in copy number in the human genome Nature444:444-54 2006 |
| PubMed ID: 17122850 |
| |
| Altshuler D, Brooks LD, Chakravarti A, Collins FS, Daly MJ, Donnelly P; International HapMap Consortium, A haplotype map of the human genome. Nature437(7063):1299-320 2005 |
| PubMed ID: 16255080 |
| |
| Miretti MM, Walsh EC, Ke X, Delgado M, Griffiths M, Hunt S, Morrison J, Whittaker P, Lander ES, Cardon LR, Bentley DR, Rioux JD, Beck S, Deloukas P, A high-resolution linkage-disequilibrium map of the human major histocompatibility complex and first generation of tag single-nucleotide polymorphisms. Am J Hum Genet76(4):634-46 2005 |
| PubMed ID: 15747258 |
| |
| Matsuzaki H, Dong S, Loi H, Di X, Liu G, Hubbell E, Law J, Berntsen T, Chadha M, Hui H, Yang G, Kennedy GC, Webster TA, Cawley S, Walsh PS, Jones KW, Fodor SP, Mei R, Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nat Methods1(2):109-11 2004 |
| PubMed ID: 15782172 |
| |
| Matsuzaki H, Dong S, Loi H, Di X, Liu G, Hubbell E, Law J, Berntsen T, Chadha M, Hui H, Yang G, Kennedy GC, Webster TA, Cawley S, Walsh PS, Jones KW, Fodor SP, Mei R, Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nat Methods1(2):109-11 2004 |
| PubMed ID: 32411386 |
|
|