Description:
PERSONAL GENOME PROJECT
|
Repository
|
No Data
|
| Subcollection |
Apparently Healthy Collection
PIGI Consented Sample |
|
License Required
|
No Data
|
|
Sample Source
|
No Data
|
|
Subject Type
|
No Data
|
|
Family Type
|
No Data
|
|
Ethnicity
|
No Data
|
|
Family Member
|
No Data
|
|
Genetic Data
|
No Data
|
| IDENTIFICATION OF SPECIES OF ORIGIN |
Species of Origin Confirmed by LINE assay |
| |
| IDENTIFICATION OF SPECIES OF ORIGIN |
Species of Origin Confirmed by LINE assay |
| |
| Chan J, Holdstock J, Shovelton J, Reid J, Speight G, Molha D, Pullabhatla V, Carpenter S, Uddin E, Washio T, Sato H, Izumi Y, Watanabe R, Niiro H, Fukushima Y, Ashida N, Hirose T, Maeda A, Clinical and analytical validation of an 82-gene comprehensive genome-profiling panel for identifying and interpreting variants responsible for inherited retinal dystrophies PloS one19:e0305422 2024 |
| PubMed ID: 38870140 |
| |
| Watanabe D, Okamoto N, Kobayashi Y, Suzuki H, Kato M, Saitoh S, Kanemura Y, Takenouchi T, Yamada M, Nakato D, Sato M, Tsunoda T, Kosaki K, Miya F, Biallelic structural variants in three patients with ERCC8-related Cockayne syndrome and a potential pitfall of copy number variation analysis Scientific reports14:19741 2024 |
| PubMed ID: 39187681 |
| |
| Greer SU, Botello J, Hongo D, Levy B, Shah P, Rabinowitz M, Miller DE, Im K, Kumar A, Implementation of Nanopore sequencing as a pragmatic workflow for copy number variant confirmation in the clinic Journal of translational medicine21:378 2023 |
| PubMed ID: 37301971 |
| |
| Li W, Huang X, Patel R, Schleifman E, Fu S, Shames DS, Zhang J, Analytical evaluation of circulating tumor DNA sequencing assays Scientific reports14:4973 2023 |
| PubMed ID: 38424110 |
| |
| 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 biotechnology14:4973 2023 |
| PubMed ID: 38740992 |
| |
| Subramanian K, Chopra M, Kahali B, Landscape of genomic structural variations in Indian population-based cohorts: Deeper insights into their prevalence and clinical relevance HGG advances5:100285 2023 |
| PubMed ID: 38521976 |
| |
| 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 |
| |
| Hernandez KM, Bramlett KS, Agius P, Baden J, Cao R, Clement O, Corner AS, Craft J, Dean DA, Dry JR, Grigaityte K, Grossman RL, Hicks J, Higa N, Holzer TR, Jensen J, Johann DJ, Katz S, Kolatkar A, Keynton JL, Lee JSH, Maar D, Martini JF, Meyer CG, Roberts PC, Ryder M, Salvatore L, Schageman JJ, Somiari S, Stetson D, Stern M, Xu L, Leiman LC, Contrived Materials and a Data Set for the Evaluation of Liquid Biopsy Tests: A Blood Profiling Atlas in Cancer (BLOODPAC) Community Study The Journal of molecular diagnostics : JMD25:143-155 2022 |
| PubMed ID: 36828596 |
| |
| Inwood SL, Tian L, Parratt K, Maragh S, Wang L, Evaluation protocol for CRISPR/Cas9-mediated CD19 knockout GM24385 cells by flow cytometry and Sanger sequencing BioTechniques72:279-286 2022 |
| PubMed ID: 35703314 |
| |
| Smullen M, Olson MN, Reichert JM, Dawes P, Murray LF, Baer CE, Wang Q, Readhead B, Church GM, Lim ET, Chan Y, Reliable multiplex generation of pooled induced pluripotent stem cells Cell reports methods3:100570 2022 |
| PubMed ID: 37751688 |
| |
| 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 |
| |
| Verner EL, Jackson JB, Severson E, Valkenburg KC, Greer AE, Riley DR, Sausen M, Maddox C, McGregor PM, Karandikar A, Hastings SB, Previs RA, Reddy VP, Jensen TJ, Ramkissoon SH, Validation of the Labcorp Plasma Focus Test to Facilitate Precision Oncology Through Cell-Free DNA Genomic Profiling of Solid Tumors The Journal of molecular diagnostics : JMD4:lqac051 2022 |
| PubMed ID: 37068734 |
| |
| Wils G, Helsmoortel C, Volders PJ, Vereecke I, Milazzo M, Vandesompele J, Coppieters F, De Leeneer K, Lefever S, Performance Evaluation of Three DNA Sample Tracking Tools in a Whole Exome Sequencing Workflow Molecular diagnosis & therapy26:411-419 2022 |
| PubMed ID: 35633488 |
| |
| 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 |
| |
| Baid G, Cook DE, Shafin K, Yun T, Llinares-López F, Berthet Q, Belyaeva A, Töpfer A, Wenger AM, Rowell WJ, Yang H, Kolesnikov A, Ammar W, Vert JP, Vaswani A, McLean CY, Nattestad M, Chang PC, Carroll A, DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer Nature biotechnology73:151-158 2021 |
| PubMed ID: 36050551 |
| |
| 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 genetics73:151-158 2021 |
| PubMed ID: 35394024 |
| |
| Eslami Rasekh M, Hernández Y, Drinan SD, Fuxman Bass JI, Benson G, Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences Nucleic acids research49:4308-4324 2021 |
| PubMed ID: 33849068 |
| |
| 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 |
| |
| Jarvis ED, Formenti G, Rhie A, Guarracino A, Yang C, Wood J, Tracey A, Thibaud-Nissen F, Vollger MR, Porubsky D, Cheng H, Asri M, Logsdon GA, Carnevali P, Chaisson MJP, Chin CS, Cody S, Collins J, Ebert P, Escalona M, Fedrigo O, Fulton RS, Fulton LL, Garg S, Gerton JL, Ghurye J, Granat A, Green RE, Harvey W, Hasenfeld P, Hastie A, Haukness M, Jaeger EB, Jain M, Kirsche M, Kolmogorov M, Korbel JO, Koren S, Korlach J, Lee J, Li D, Lindsay T, Lucas J, Luo F, Marschall T, Mitchell MW, McDaniel J, Nie F, Olsen HE, Olson ND, Pesout T, Potapova T, Puiu D, Regier A, Ruan J, Salzberg SL, Sanders AD, Schatz MC, Schmitt A, Schneider VA, Selvaraj S, Shafin K, Shumate A, Stitziel NO, Stober C, Torrance J, Wagner J, Wang J, Wenger A, Xiao C, Zimin AV, Zhang G, Wang T, Li H, Garrison E, Haussler D, Hall I, Zook JM, Eichler EE, Phillippy AM, Paten B, Howe K, Miga KH, Human Pangenome Reference Consortium KH, Semi-automated assembly of high-quality diploid human reference genomes Nature611:519-531 2021 |
| PubMed ID: 36261518 |
| |
| 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 Cell611:519-531 2021 |
| PubMed ID: 35525246 |
| |
| Ralf A, Zandstra D, Weiler N, van Ijcken WFJ, Sijen T, Kayser M, RMplex: An efficient method for analyzing 30 Y-STRs with high mutation rates Forensic science international Genetics55:102595 2021 |
| PubMed ID: 34543845 |
| |
| 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 |
| |
| Sakamoto Y, Miyake S, Oka M, Kanai A, Kawai Y, Nagasawa S, Shiraishi Y, Tokunaga K, Kohno T, Seki M, Suzuki Y, Suzuki A, Phasing analysis of lung cancer genomes using a long read sequencer Nature communications13:3464 2021 |
| PubMed ID: 35710642 |
| |
| Wagner J, Olson ND, Harris L, McDaniel J, Cheng H, Fungtammasan A, Hwang YC, Gupta R, Wenger AM, Rowell WJ, Khan ZM, Farek J, Zhu Y, Pisupati A, Mahmoud M, Xiao C, Yoo B, Sahraeian SME, Miller DE, Jáspez D, Lorenzo-Salazar JM, Muñoz-Barrera A, Rubio-Rodríguez LA, Flores C, Narzisi G, Evani US, Clarke WE, Lee J, Mason CE, Lincoln SE, Miga KH, Ebbert MTW, Shumate A, Li H, Chin CS, Zook JM, Sedlazeck FJ, Curated variation benchmarks for challenging medically relevant autosomal genes Nature biotechnology40:672-680 2021 |
| PubMed ID: 35132260 |
| |
| 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 chemistry40:672-680 2020 |
| PubMed ID: 32395759 |
| |
| Park J, Kim HS, Lee JM, Jung J, Kang D, Choi H, Lee GD, Son J, Park S, Cho BS, Kim HJ, Kim S, Lee JW, Chung NG, Cho B, Zhang H, Khazanov NA, Choi J, Jung JW, Kim Y, Kim M, Analytical and Potential Clinical Performance of Oncomine Myeloid Research Assay for Myeloid Neoplasms Molecular diagnosis & therapy40:672-680 2020 |
| PubMed ID: 32676933 |
| |
| Reis ALM, Deveson IW, Wong T, Madala BS, Barker C, Blackburn J, Marcellin E, Mercer TR, A universal and independent synthetic DNA ladder for the quantitative measurement of genomic features Nature communications11:3609 2020 |
| PubMed ID: 32681090 |
| |
| Shafin K, Pesout T, Lorig-Roach R, Haukness M, Olsen HE, Bosworth C, Armstrong J, Tigyi K, Maurer N, Koren S, Sedlazeck FJ, Marschall T, Mayes S, Costa V, Zook JM, Liu KJ, Kilburn D, Sorensen M, Munson KM, Vollger MR, Monlong J, Garrison E, Eichler EE, Salama S, Haussler D, Green RE, Akeson M, Phillippy A, Miga KH, Carnevali P, Jain M, Paten B, Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes Nature biotechnology38:1044-1053 2020 |
| PubMed ID: 32686750 |
| |
| 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 & therapy38:1044-1053 2019 |
| PubMed ID: 31209714 |
| |
| 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 research38:1044-1053 2019 |
| PubMed ID: 32540955 |
| |
| 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 : JMD38:1044-1053 2019 |
| PubMed ID: 31445212 |
| |
| 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 biotechnology38:1044-1053 2019 |
| PubMed ID: 32541958 |
| |
| 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 |
| |
| Vegesna R, Tomaszkiewicz M, Medvedev P, Makova KD, Dosage regulation, and variation in gene expression and copy number of human Y chromosome ampliconic genes PLoS genetics15:e1008369 2019 |
| PubMed ID: 31525193 |
| |
| Yavas G, Hong H, Xiao W, dnAQET: a framework to compute a consolidated metric for benchmarking quality of de novo assemblies BMC genomics20:706 2019 |
| PubMed ID: 31510940 |
| |
| 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 |
| |
| Filges S, Yamada E, Ståhlberg A, Godfrey TE, Impact of Polymerase Fidelity on Background Error Rates in Next-Generation Sequencing with Unique Molecular Identifiers/Barcodes Scientific reports9:3503 2018 |
| PubMed ID: 30837525 |
| |
| He HJ, Stein EV, Konigshofer Y, Forbes T, Tomson FL, Garlick R, Yamada E, Godfrey T, Abe T, Tamura K, Borges M, Goggins M, Elmore S, Gulley ML, Larson JL, Ringel L, Haynes BC, Karlovich C, Williams PM, Garnett A, Ståhlberg A, Filges S, Sorbara L, Young MR, Srivastava S, Cole KD, Multilaboratory Assessment of a New Reference Material for Quality Assurance of Cell-Free Tumor DNA Measurements The Journal of molecular diagnostics : JMD21:658-676 2018 |
| PubMed ID: 31055023 |
| |
| 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 : JMD21:658-676 2018 |
| PubMed ID: 30610921 |
| |
| 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 |
| |
| Salcedo A, Tarabichi M, Espiritu SMG, Deshwar AG, David M, Wilson NM, Dentro S, Wintersinger JA, Liu LY, Ko M, Sivanandan S, Zhang H, Zhu K, Ou Yang TH, Chilton JM, Buchanan A, Lalansingh CM, P'ng C, Anghel CV, Umar I, Lo B, Zou W, DREAM SMC-Het Participants W, Simpson JT, Stuart JM, Anastassiou D, Guan Y, Ewing AD, Ellrott K, Wedge DC, Morris Q, Van Loo P, Boutros PC, A community effort to create standards for evaluating tumor subclonal reconstruction Nature biotechnology38:97-107 2018 |
| PubMed ID: 31919445 |
| |
| 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 |
| |
| 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 |
| |
| Mao Q, Ciotlos S, Zhang RY, Ball MP, Chin R, Carnevali P, Barua N, Nguyen S, Agarwal MR, Clegg T, Connelly A, Vandewege W, Zaranek AW, Estep PW, Church GM, Drmanac R, Peters BA., The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes. Gigascience.5(1):42 2016 |
| PubMed ID: 27724973 |
| |
| Church GM, The personal genome project. Mol Syst Biol.1, 2005.0030:42 2005 |
| PubMed ID: 16729065 |
| Split Ratio |
1:4 |
| Temperature |
37 C |
| Percent CO2 |
5% |
| Percent O2 |
AMBIENT |
| Medium |
Roswell Park Memorial Institute Medium 1640 with 2mM L-glutamine or equivalent |
| Serum |
15% fetal bovine serum Not Inactivated |
| Substrate |
None specified |
| Subcultivation Method |
dilution - add fresh medium |
| Supplement |
- |
|
|