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Research: Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications
- Judith Arres,
- Santosh Elavalli,
- Shalini Behl,
- Daniel Matias Sanchez,
- Ayesha Al Ali,
- Abdelrahman Ahmed Yehia Abdelaziz Saad,
- Azza Attia,
- Cyla Minas,
- Sharika Pariyachery,
- Shariq Ahmed,
- Fatmah Aldhuhoori,
- Nitu Thulasidharan,
- Gurunath Katagi,
- Omar Soliman,
- Shilp Purohit,
- Vinay Kusuma,
- Raony Cardenas,
- Thyago Cardoso,
- Luis F. Paulin,
- Philippe Sanio,
- Joseph Mafofo,
- Haiguo Wu,
- Val Zvereff,
- Albarah El-Khani,
- Fahed Al Marzooqi,
- Tiago R. Magalhães,
- Fritz J. Sedlazeck,
- and Javier Quilez
Genome Res. March 2026 36: 460-471; Published in Advance February 11, 2026, doi:10.1101/gr.280134.124
...to resolve pathogenic alleles within homologous regions, SVs, or STRs. In many cases, the reported SNV is merely in linkage disequilibrium with a more complex causative variant—such as a copy number variant (CNV) or small insertion or deletion (indel) in a paralogous gene or deep intronic rearrangement...
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Research: A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxia
- Haloom Rafehi,
- Liam G. Fearnley,
- Justin Read,
- Penny Snell,
- Kayli C. Davies,
- Liam Scott,
- Greta Gillies,
- Genevieve C. Thompson,
- Tess A. Field,
- Aleena Eldo,
- Simon Bodek,
- Ernest Butler,
- Luke Chen,
- John Drago,
- Himanshu Goel,
- Anna Hackett,
- G. Michael Halmagyi,
- Andrew Hannaford,
- Katya Kotschet,
- Kishore R. Kumar,
- Smitha Kumble,
- Matthew Lee-Archer,
- Abhishek Malhotra,
- Mark Paine,
- Michael Poon,
- Kate Pope,
- Katrina Reardon,
- Steven Ring,
- Anne Ronan,
- Matthew Silsby,
- Renee Smyth,
- Chloe Stutterd,
- Mathew Wallis,
- John Waterston,
- Thomas Wellings,
- Kirsty West,
- Christine Wools,
- Kathy H.C. Wu,
- David J. Szmulewicz,
- Martin B. Delatycki,
- Melanie Bahlo,
- and Paul J. Lockhart
Genome Res. April 2025 35: 769-785; Published in Advance February 27, 2025, doi:10.1101/gr.279634.124
...(Supplemental Table S1). We tested for the possibility of a second pathogenic small variant or CNV on the other FXN allele utilizing research tools seqr and CXGo; however, no candidate variants were identified, suggesting these individuals are heterozygous carriers. Testing for the nonreference pathogenic AAGGG...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...the diagnostic utility of LRS. By enabling the simultaneous detection of SNVs, SVs, CNVs, and DNA modifications, it allows disease mechanisms that previously required separate specialized tests to be studied under a single, unified approach, such as imprinting (A), epimutations (B), and repeat expansions (C...
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Research: Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders
- Susan M. Hiatt,
- James M.J. Lawlor,
- Lori H. Handley,
- Donald R. Latner,
- Zachary T. Bonnstetter,
- Candice R. Finnila,
- Michelle L. Thompson,
- Lori Beth Boston,
- Melissa Williams,
- Ivan Rodriguez Nunez,
- Jerry Jenkins,
- Whitley V. Kelley,
- E. Martina Bebin,
- Michael A. Lopez,
- Anna C.E. Hurst,
- Bruce R. Korf,
- Jeremy Schmutz,
- Jane Grimwood,
- and Gregory M. Cooper
Genome Res. November 2024 34: 1747-1762; Published in Advance September 19, 2024, doi:10.1101/gr.279227.124
...published gene-disease associations. Seven cases included variants that were only correctly interpreted in lrGS, including copy-number variants (CNVs), an inversion, a mobile element insertion, two low-complexity repeat expansions, and a 1 bp deletion. While evidence for each of these variants is...
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Method: A novel method for detecting uniparental disomy from trio genotypes identifies a significant excess in children with developmental disorders
- Daniel A. King,
- Tomas W. Fitzgerald,
- Ray Miller,
- Natalie Canham,
- Jill Clayton-Smith,
- Diana Johnson,
- Sahar Mansour,
- Fiona Stewart,
- Pradeep Vasudevan,
- Matthew E. Hurles,
- and the DDD Study
Genome Res. April 2014 24: 673-687; Published in Advance December 19, 2013, doi:10.1101/gr.160465.113
...) candidate variant selection (Fig. 1). Genotype preparation beginswith preprocessing the genotype data fromSNP chip or exome sequencing data. Data preprocessing is critical and includes two steps: (1) removal of low-quality genotypes, (2) removal of genotyped sites within CNVs, since heterozygous deletions...
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Method: Predicting human genes susceptible to genomic instability associated with Alu/Alu-mediated rearrangements
- Xiaofei Song,
- Christine R. Beck,
- Renqian Du,
- Ian M. Campbell,
- Zeynep Coban-Akdemir,
- Shen Gu,
- Amy M. Breman,
- Pawel Stankiewicz,
- Grzegorz Ira,
- Chad A. Shaw,
- and James R. Lupski
Genome Res. August 2018 28: 1228-1242; Published in Advance June 15, 2018, doi:10.1101/gr.229401.117
...://alualucnvpredictor.research.bcm.edu:3838).We annotated the hotspot genes for human disease phenotypes using OMIM. The known disease relevant genes (77 out of 329) are listed in Table 2 (in alphabetical order). Of the 77 OMIM entries, 33 are associated with recessive disease traits, in which a CNV-Alu mediated exonic deletion may...
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Method: A comprehensively molecular haplotype-resolved genome of a European individual
- Eun-Kyung Suk,
- Gayle K. McEwen,
- Jorge Duitama,
- Katja Nowick,
- Sabrina Schulz,
- Stefanie Palczewski,
- Stefan Schreiber,
- Dustin T. Holloway,
- Stephen McLaughlin,
- Heather Peckham,
- Clarence Lee,
- Thomas Huebsch,
- and Margret R. Hoehe
Genome Res. October 2011 21: 1672-1685; Published in Advance August 3, 2011, doi:10.1101/gr.125047.111
...variants (SVs) inserting or deleting up to ;1-kb DNA sequence and 148 copy number variants (CNVs) were identified (Supplemental Table S7). MP1’s variation profile is generally consistent with European ancestry including the s of Watson (Wheeler et al. 2008) and Venter (Levy et al. 2007) (Supplemental Table...
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Method: A general framework for identifying oligogenic combinations of rare variants in complex disorders
- Vijay Kumar Pounraja and
- Santhosh Girirajan
Genome Res. May 2022 32: 904-915; Published in Advance March 17, 2022, doi:10.1101/gr.276348.121
...is often overlooked. Variants in this category are often transmitted across generations without adverse effects on their carriers until they encounter other similar variants that, when combined, lead to genetic interactions conferring a higher risk for disease than their individual risks (Badano...
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Method: Bayesian-based noninvasive prenatal diagnosis of single-gene disorders
- Tom Rabinowitz,
- Avital Polsky,
- David Golan,
- Artem Danilevsky,
- Guy Shapira,
- Chen Raff,
- Lina Basel-Salmon,
- Reut Tomashov Matar,
- and Noam Shomron
Genome Res. March 2019 29: 428-438; Published in Advance February 20, 2019, doi:10.1101/gr.235796.118
...-free DNA fragment-size distribution analysis for non-invasive prenatal CNV prediction. Bioinformatics 32: 1662–1669. doi:10.1093/bioinformatics/btw178 ↵Belkadi A, Bolze A, Itan Y, Cobat A, Vincent QB, Antipenko A, Shang L, Boisson B, Casanova JL, Abel L. 2015. Whole- sequencing is more powerful than whole...
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Research: Actionable exomic incidental findings in 6503 participants: challenges of variant classification
- Laura M. Amendola,
- Michael O. Dorschner,
- Peggy D. Robertson,
- Joseph S. Salama,
- Ragan Hart,
- Brian H. Shirts,
- Mitzi L. Murray,
- Mari J. Tokita,
- Carlos J. Gallego,
- Daniel Seung Kim,
- James T. Bennett,
- David R. Crosslin,
- Jane Ranchalis,
- Kelly L. Jones,
- Elisabeth A. Rosenthal,
- Ella R. Jarvik,
- Andy Itsara,
- Emily H. Turner,
- Daniel S. Herman,
- Jennifer Schleit,
- Amber Burt,
- Seema M. Jamal,
- Jenica L. Abrudan,
- Andrew D. Johnson,
- Laura K. Conlin,
- Matthew C. Dulik,
- Avni Santani,
- Danielle R. Metterville,
- Melissa Kelly,
- Ann Katherine M. Foreman,
- Kristy Lee,
- Kent D. Taylor,
- Xiuqing Guo,
- Kristy Crooks,
- Lesli A. Kiedrowski,
- Leslie J. Raffel,
- Ora Gordon,
- Kalotina Machini,
- Robert J. Desnick,
- Leslie G. Biesecker,
- Steven A. Lubitz,
- Surabhi Mulchandani,
- Greg M. Cooper,
- Steven Joffe,
- C. Sue Richards,
- Yaoping Yang,
- Jerome I. Rotter,
- Stephen S. Rich,
- Christopher J. O’Donnell,
- Jonathan S. Berg,
- Nancy B. Spinner,
- James P. Evans,
- Stephanie M. Fullerton,
- Kathleen A. Leppig,
- Robin L. Bennett,
- Thomas Bird,
- Virginia P. Sybert,
- William M. Grady,
- Holly K. Tabor,
- Jerry H. Kim,
- Michael J. Bamshad,
- Benjamin Wilfond,
- Arno G. Motulsky,
- C. Ronald Scott,
- Colin C. Pritchard,
- Tom D. Walsh,
- Wylie Burke,
- Wendy H. Raskind,
- Peter Byers,
- Fuki M. Hisama,
- Heidi Rehm,
- Debbie A. Nickerson,
- and Gail P. Jarvik
Genome Res. March 2015 25: 305-315; Published in Advance January 30, 2015, doi:10.1101/gr.183483.114
...and agreement was high (97/ 99, 98%) (Supplemental Table 4). A summary of the evidence supporting the two Table 2. Highest ancestry-specific minor allele frequency (MAF) in EVS of HGMD disease-causing variants in dominant genes by variant classification Pathogenic Likely pathogenic Uncertain significance Likely...
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