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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
...can have clinical/biological consequences. TR instabilities occur in humans and other organisms. TRs can be epigenetically modified and/or chromosomal fragile sites. We discuss the expanding field of disease-associated TR instabilities, highlighting prospects, clinical and genetic clues, tools...
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Resource: Recent, full-length gene retrocopies are common in canids
- Kevin Batcher,
- Scarlett Varney,
- Daniel York,
- Matthew Blacksmith,
- Jeffrey M. Kidd,
- Robert Rebhun,
- Peter Dickinson,
- and Danika Bannasch
Genome Res. August 2022 32: 1602-1611; Published in Advance August 12, 2022, doi:10.1101/gr.276828.122
...the location of retroCNV parent genes and their insertion sites, with links colored based on the chromosome of the parent gene. (A) All recent retroCNVs identified in canids with no retroCNV-specific variants. (B) All retroCNVs of the GAP43 parent gene. (C) All retroCNVs present in a single Golden Retriever...
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Resource: Impact of regulatory variation across human iPSCs and differentiated cells
- Nicholas E. Banovich,
- Yang I. Li,
- Anil Raj,
- Michelle C. Ward,
- Peyton Greenside,
- Diego Calderon,
- Po Yuan Tung,
- Jonathan E. Burnett,
- Marsha Myrthil,
- Samantha M. Thomas,
- Courtney K. Burrows,
- Irene Gallego Romero,
- Bryan J. Pavlovic,
- Anshul Kundaje,
- Jonathan K. Pritchard,
- and Yoav Gilad
Genome Res. January 2018 28: 122-131; Published in Advance December 5, 2017, doi:10.1101/gr.224436.117
...the regulatory effects of disease-associated variants.Here, we report the reprogramming of 58 Yoruba lymphoblastoid cell lines (LCLs) into iPSCs, of which 14 were further differentiated into cardiomyocytes. Previously, our group extensively studied gene regulatory variation in the Yoruba LCLs. The establishment...
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Perspective: Non-Darwinian estimation: My ancestors, my genes' ancestors
- Kenneth M. Weiss and
- Jeffrey C. Long
Genome Res. May 2009 19: 703-710; doi:10.1101/gr.076539.108
...in recent disease association studies, as well as longer term history of our species including intercontinental migrations and founder events (see Wright 1969). Darwinian and platonic concepts of variation There are many ways to portray the degrees of genetic similarity and relationships among a set...
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Method: Quantification of GC-biased gene conversion in the human genome
- Sylvain Glémin,
- Peter F. Arndt,
- Philipp W. Messer,
- Dmitri Petrov,
- Nicolas Galtier,
- and Laurent Duret
Genome Res. August 2015 25: 1215-1228; Published in Advance May 20, 2015, doi:10.1101/gr.185488.114
...and dominance coefficients (Glémin 2010). Accordingly, gBGC tracts are enriched in disease-associated polymorphisms (Capra et al. 2013), and W → S disease-causing mutations segregate at higher frequency than S → W mutations (Necsulea et al. 2011; Lachance and Tishkoff 2014). High rates of fixation...
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Method: Read clouds uncover variation in complex regions of the human genome
- Alex Bishara,
- Yuling Liu,
- Ziming Weng,
- Dorna Kashef-Haghighi,
- Daniel E. Newburger,
- Robert West,
- Arend Sidow,
- and Serafim Batzoglou
Genome Res. October 2015 25: 1570-1580; Published in Advance August 18, 2015, doi:10.1101/gr.191189.115
...al. 2002). These regions tend to be hotspots of structural and copy number variants (CNVs) (Coe et al. 2014; Chaisson et al. 2015) that in aggregate affect a larger fraction of the than that affected by single nucleotide polymorphisms (SNPs) (Conrad et al. 2010). CNVs have been associated...
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Letter: Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes
- David L. Goode,
- Gregory M. Cooper,
- Jeremy Schmutz,
- Mark Dickson,
- Eidelyn Gonzales,
- Ming Tsai,
- Kalpana Karra,
- Eugene Davydov,
- Serafim Batzoglou,
- Richard M. Myers,
- and Arend Sidow
Genome Res. March 2010 20: 301-310; Published in Advance January 12, 2010, doi:10.1101/gr.102210.109
...functional variants. We resequenced 575 amplicons within 432 individuals at genomic sites enriched for evolutionary constraint and also analyzed variation within three published human genomes. We find that single-site measures of evolutionary constraint derived from mammalian multiple sequence alignments...
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Method: Full-resolution HLA and KIR gene annotations for human genome assemblies
- Ying Zhou,
- Li Song,
- and Heng Li
Genome Res. November 2024 34: 1931-1941; Published in Advance June 5, 2024, doi:10.1101/gr.278985.124
...of the HLA class I region spanning the HLA-E-to-HLA-F interval by using yeast artificial chromosomes. Proc Natl Acad Sci 89: 2669–2673. doi:10.1073/pnas.89.7.2669 ↵Gough SCL, Simmonds MJ. 2007. The HLA region and autoimmune disease: associations and mechanisms of action. Curr Genomics 8: 453–465. doi:10...
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Research: Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate
- Wilfried M. Guiblet,
- Marzia A. Cremona,
- Monika Cechova,
- Robert S. Harris,
- Iva Kejnovská,
- Eduard Kejnovsky,
- Kristin Eckert,
- Francesca Chiaromonte,
- and Kateryna D. Makova
Genome Res. December 2018 28: 1767-1778; Published in Advance November 6, 2018, doi:10.1101/gr.241257.118
...Zhao et al. 2010; Bacolla et al. 2011; Inagaki et al. 2013), at disease-associated genes (Kamat et al. 2016), and among genetic variants from the 1000 Genomes Project (Du et al. 2014). Because the effect of non-B DNA on mutagenesis is driven by both the inherent DNA sequence and polymerase fidelity...
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REVIEW: Defensins and the dynamic genome: What we can learn from structural variation at human chromosome band 8p23.1
- Edward J. Hollox,
- John C.K. Barber,
- Anthony J. Brookes,
- and John A.L. Armour
Genome Res. November 2008 18: 1686-1697; doi:10.1101/gr.080945.108
...-allelic recombination (NAHR) or gene conversion within this array ( Fig. 2 ) ( Aldred et al. 2005 ). In native UK individuals, DEFA3 variant is absent in 10% of the population, and in sub-Saharan Africans (Yoruba), it is absent in 37% of the population. DEFA3 absence is associated with one SNP haplotype in Europeans...

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