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Method: Parente2: a fast and accurate method for detecting identity by descent
- Jesse M. Rodriguez,
- Sivan Bercovici,
- Lin Huang,
- Roy Frostig,
- and Serafim Batzoglou
Genome Res. February 2015 25: 280-289; Published in Advance October 1, 2014, doi:10.1101/gr.173641.114
...has higher statistical power to detect disease susceptibility genes when multiple rare causal variants cluster within them (Browning and Thompson 2012). Extensive previous work has focused on developing methods for IBD segment detection. One of the earlier methods, PLINK (Purcell et al. 2007), uses...
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Method: A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis
- Ruhollah Shemirani,
- Gillian M. Belbin,
- Sinead Cullina,
- Christa Caggiano,
- Christopher R. Gignoux,
- Noah Zaitlen,
- and Eimear E. Kenny
Genome Res. March 2026 36: 534-546; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125
...structure and the complex genetic architecture they reveal.To address these limitations, estimates of pairwise haplotypes shared identical-by-descent, or identity-by-descent (IBD), offer a more precise approach for detecting recent fine-scale population structure in large genomic data sets (Shemirani et al...
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RESOURCE: Detecting genetic variation in microarray expression data
- Jennifer A. Greenhall,
- Matthew A. Zapala,
- Mario Cáceres,
- Ondrej Libiger,
- Carrolee Barlow,
- Nicholas J. Schork,
- and David J. Lockhart
Genome Res. August 2007 17: 1228-1235; Published in Advance July 3, 2007, doi:10.1101/gr.6307307
...– 10678 . ↵ Giallourakis, C. , Stoll, M. , Miller, K. , Hampe, J. , Lander, E.S. , Daly, M.J. , Schreiber, S. , Rioux, J.D. ( 2003 ) IBD5 is a general risk factor for inflammatory bowel disease: Replication of association with Crohn disease and identification of a novel association with ulcerative colitis...
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Research: Autozygome-guided exome sequencing in retinal dystrophy patients reveals pathogenetic mutations and novel candidate disease genes
- Leen Abu-Safieh,
- May Alrashed,
- Shamsa Anazi,
- Hisham Alkuraya,
- Arif O. Khan,
- Mohammed Al-Owain,
- Jawahir Al-Zahrani,
- Lama Al-Abdi,
- Mais Hashem,
- Salwa Al-Tarimi,
- Mohammed-Adeeb Sebai,
- Ahmed Shamia,
- Mohamed D. Ray-zack,
- Malik Nassan,
- Zuhair N. Al-Hassnan,
- Zuhair Rahbeeni,
- Saad Waheeb,
- Abdullah Alkharashi,
- Emad Abboud,
- Selwa A.F. Al-Hazzaa,
- and Fowzan S. Alkuraya
Genome Res. February 2013 23: 236-247; Published in Advance October 26, 2012, doi:10.1101/gr.144105.112
..., as we show in this study, the distinction of IBS and IBD can be challenging (Alkuraya 2012). Next-generation sequencing allows massively parallel sequencing at an unprecedented scale both in throughput and cost and has recently been used on a smaller scale in the study of retinal dystrophy genetics...
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Method: Aberrant landscapes of maternal meiotic crossovers contribute to aneuploidies in human embryos
- Daniel Ariad,
- Svetlana Madjunkova,
- Mitko Madjunkov,
- Siwei Chen,
- Rina Abramov,
- Clifford Librach,
- and Rajiv C. McCoy
Genome Res. January 2024 34: 70-84; Published in Advance December 1, 2023, doi:10.1101/gr.278168.123
...the genomic locations of meiotic recombination events is to compare genotype data from related individuals. Such data can be scanned to identify regions where haplotypes match (i.e., are identical by descent [IBD]). The boundaries of the matched haplotypes reflect the locations of meiotic crossovers...
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Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
- Reuben M. Buckley and
- Elaine A. Ostrander
Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
....Although the absence of particular breeds from large WGS cohorts can be indicative of missing variation, genetic variants from unsampled breeds can often be found within closely related breeds that share recent common ancestry reflecting shared identity-by-descent (IBD) segments (Parker et al. 2017). This is evidenced...
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Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
- Alejandro Martin-Trujillo,
- Paras Garg,
- Nihir Patel,
- Bharati Jadhav,
- and Andrew J. Sharp
Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
...is the primary cause of AD according to the amyloid hypothesis. We also observed an association between a CCG repeat (Chr 7: 99,144,016–99,144,048) in the promoter of SMURF1 [MIM: 605568] and inflammatory bowel disease (IBD). SMURF1, which encodes for an E3 ubiquitin ligase and acts as a mediator of autophagy...
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Method: Microbial strain-level population structure and genetic diversity from metagenomes
- Duy Tin Truong,
- Adrian Tett,
- Edoardo Pasolli,
- Curtis Huttenhower,
- and Nicola Segata
Genome Res. April 2017 27: 626-638; Published in Advance February 6, 2017, doi:10.1101/gr.216242.116
...et al. 2014), which includes 66 longitudinally sampled patients with inflammatory bowel disease (IBD). To this end, we defined ourmeasure of genetic distance between strains as the length-normalized rate of singlenucleotide variants (SNVs) between the full set of markers considered in each species...
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Method: Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets
- Qing Xiong,
- Nicola Ancona,
- Elizabeth R. Hauser,
- Sayan Mukherjee,
- and Terrence S. Furey
Genome Res. February 2012 22: 386-397; Published in Advance September 22, 2011, doi:10.1101/gr.124370.111
...-Neriah and Schmidt-Supprian 2007; Nenci et al. 2007; Zaph et al. 2007; Atreya et al. 2008; Spehlmann and Eckmann 2009). Deficiency in or hyperactivation of NFKB is one of the core mechanisms leading to chronic inflammatory bowel disease (IBD). NFKB signaling is primarily regulated by inhibitory IκB proteins...
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Research: Unique genetic basis of the distinct antibiotic potency of high acetic acid production in the probiotic yeast Saccharomyces cerevisiae var. boulardii
- Benjamin Offei,
- Paul Vandecruys,
- Stijn De Graeve,
- María R. Foulquié-Moreno,
- and Johan M. Thevelein
Genome Res. September 2019 29: 1478-1494; Published in Advance August 29, 2019, doi:10.1101/gr.243147.118
...obscure. It is considered conspecific with budding yeast Saccharomyces cerevisiae, which is generally used in classical food applications. They have an almost identical sequence, making the genetic basis of probiotic potency in S. boulardii puzzling. We now show that S. boulardii produces at 37°C...
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