Validation of the first PGT-whole genome sequencing approach including mitochondrial variants
Yu Xia,Dhruva Chandramohan,Willy Chertman,Elan Bechor,Robert Maier,Noor Siddiqui,Barry Behr,Justin B. Schleede +7 more
TLDR
The ability to improve the accuracy of certain types of mendelian variants in the authors' data to close to 100% is demonstrated by leveraging parental and a born child’s genome to perform linkage analysis.Abstract:
Whole genome screening is currently not available in preimplantation genetic testing (PGT) due to poor performance of whole genome amplification methods. Here, we present the first validation study using our latest whole genome amplification (WGA) protocol, which yields amplified DNA with comparable quality to genomic DNA when perfoming whole genome sequencing assays. We started by validating PGT for aneuploidy (PGT-A) using our WGA protocol on cell lines and donated human embryos, where amplification success rates were >99.9% and 96.2% respectively. Accuracy on both was >99.9% on aneuploidy status. We next validated whole genome sequencing using amplified and genomic DNA from the Genome in the Bottle reference sample NA12878 to demonstrate accuracy, specificity, sensitivity, and precision of our WGA methods. Amplified DNA and genomic DNA are comparable in this case, with 99.99% accuracy, 99.99% specificity, 98.0% sensitivity and 98.1% precision with our WGA protocol. We additionally examined variant calls between biopsies and the remaining embryos from which they were derived. Again, 99.99% accuracy, 99.99% specificity, 98.1% sensitivity and 98.0% precision were observed. Mitochondrial heteroplasmy between biopsies and embryos was validated, and 99.9% accuracy, 100% specificity, 99.1% sensitivity and 100% precision were observed. Finally, we demonstrated the ability to improve the accuracy of certain types of mendelian variants in our data to close to 100% by leveraging parental and a born child’s genome to perform linkage analysis.read more
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Journal ArticleDOI
Genome-wide polygenic scores for common diseases identify individuals with risk equivalent to monogenic mutations
Amit Khera,Mark Chaffin,Krishna G. Aragam,Mary E. Haas,Carolina Roselli,Seung Hoan Choi,Pradeep Natarajan,Eric S. Lander,Steven A. Lubitz,Steven A. Lubitz,Patrick T. Ellinor,Patrick T. Ellinor,Sekar Kathiresan +12 more
TL;DR: Genome-wide polygenic risk scores derived from GWAS data for five common diseases can identify subgroups of the population with risk approaching or exceeding that of a monogenic mutation.
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Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications
TL;DR: Five commercial WGA kits are compared by performing deep sequencing of multiple single cells and several major applications of single-cell genomics are discussed, including studies of whole-genome de novo mutation rates, the early evolution of cancer genomes, circulating tumor cells, meiotic recombination of germ cells, preimplantation genetic diagnosis (PGD), and preim implantation genomic screening (PGS) for in vitro-fertilized embryos.
Journal ArticleDOI
Prenatal and pre-implantation genetic diagnosis
TL;DR: Genome-wide single-cell arrays and high-throughput sequencing analyses are dramatically increasing the ability to detect embryonic and fetal genetic lesions, and have substantially improved embryo selection for in vitro fertilization.
Journal ArticleDOI
Preimplantation genetic diagnosis in mitochondrial DNA disorders: challenge and success
Suzanne C E H Sallevelt,Joseph C F M Dreesen,Joseph C F M Dreesen,Marion Drüsedau,Sabine Spierts,Edith Coonen,Edith Coonen,Florence H J van Tienen,Florence H J van Tienen,Ronald J T van Golde,Irineus F. M. de Coo,Joep P.M. Geraedts,Joep P.M. Geraedts,Christine E. M. de Die-Smulders,Christine E. M. de Die-Smulders,Hubert J.M. Smeets,Hubert J.M. Smeets +16 more
TL;DR: PGD provides carriers of mtDNA mutations the opportunity to conceive healthy offspring through preimplantation genetic diagnosis, which circumvents these problems by transferring an embryo below the threshold of clinical expression.
Posted ContentDOI
Benchmarking challenging small variants with linked and long reads
Justin Wagner,Nathan D. Olson,Lindsay Harris,Ziad Khan,Jesse Farek,Medhat Mahmoud,Ana Stankovic,Vladimir Kovacevic,Aaron M. Wenger,William J Rowell,Chunlin Xiao,Byunggil Yoo,Neil A. Miller,Jeffrey A. Rosenfeld,Bohan Ni,Samantha Zarate,Melanie Kirsche,Sergey Aganezov,Michael C. Schatz,Giuseppe Narzisi,Marta Byrska-Bishop,Wayne E. Clarke,Uday S. Evani,Charles Markello,Kishwar Shafin,Xin Zhou,Arend Sidow,Vikas Bansal,Peter Ebert,Tobias Marschall,Peter M. Lansdorp,Vincent C. T. Hanlon,Carl-Adam Mattsson,Alvaro Martinez Barrio,Ian T. Fiddes,Arkarachai Fungtammasan,Chen-Shan Chin,Fritz J. Sedlazeck,Andrew Carroll,Marc L. Salit,Justin M. Zook +40 more
TL;DR: The utility of this GIAB benchmark is demonstrated to assess performance in more challenging regions, which enables benchmarking in more difficult genes and continued technology and bioinformatics development.