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Method: Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing
- Sena A. Gocuk,
- James Lancaster,
- Shian Su,
- Jasleen K. Jolly,
- Thomas L. Edwards,
- Doron G. Hickey,
- Matthew E. Ritchie,
- Marnie E. Blewitt,
- Lauren N. Ayton,
- and Quentin Gouil
Genome Res. November 2024 34: 1954-1965; Published in Advance September 16, 2024, doi:10.1101/gr.279396.124
...hundred bases of each read are live-basecalled and mapped to the reference. If the sequence maps to the X Chromosome, sequencing of that read is allowed to continue, whereas if the sequence does not map or maps elsewhere, the read is deemed off-target and its sequencing is interrupted by voltage reversal...
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Research: Mosaic loss of Chromosome Y in aged human microglia
- Michael C. Vermeulen,
- Richard Pearse,
- Tracy Young-Pearse,
- and Sara Mostafavi
Genome Res. October 2022 32: 1795-1807; Published in Advance August 30, 2022, doi:10.1101/gr.276409.121
...). Reads were aligned to the GRCh38 2020-A reference (10x Genomics) using Cellranger count in intron-retaining mode. To include intronic reads, we used the “–include-introns” flag. This flag considers confidently mapped intronic reads as candidates for UMI counting. Although the use of intronic reads...
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Research: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
- Jian-Hai Chen,
- Patrick Landback,
- Deanna Arsala,
- Alexander Guzzetta,
- Shengqian Xia,
- Jared Atlas,
- Dylan Sosa,
- Yong E. Zhang,
- Jingqiu Cheng,
- Bairong Shen,
- and Manyuan Long
Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
...). To date, more than 4000 Mendelian disease genes have been identified, each contributing to a diverse array of human phenotypes (Boycott et al. 2013; https://mirror.omim.org/statistics/geneMap). These disease genes and associated phenotypes could provide insights into the evolutionary trajectory of human...
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Research: Large palindromes on the primate X Chromosome are preserved by natural selection
- Emily K. Jackson,
- Daniel W. Bellott,
- Ting-Jan Cho,
- Helen Skaletsky,
- Jennifer F. Hughes,
- Tatyana Pyntikova,
- and David C. Page
Genome Res. August 2021 31: 1337-1352; Published in Advance July 21, 2021, doi:10.1101/gr.275188.120
...(Kuroda-Kawaguchi et al. 2001; Bellott et al. 2018). Recently, the incorporation of ultralong nanopore reads into a clone-based sequencing approach (Single Haplotype Iterative Mapping and Sequencing 3.0, or SHIMS 3.0) has enabled the time- and cost-effective resolution of amplicons, including the TSPY1...
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Method: Inferring genes that escape X-Chromosome inactivation reveals important contribution of variable escape genes to sex-biased diseases
- Renan Sauteraud,
- Jill M. Stahl,
- Jesica James,
- Marisa Englebright,
- Fang Chen,
- Xiaowei Zhan,
- Laura Carrel,
- and Dajiang J. Liu
Genome Res. September 2021 31: 1629-1637; Published in Advance August 23, 2021, doi:10.1101/gr.275677.121
...% of the subjects (SEPTIN6, STK26, and MAP7D2). It is notable, however, that other studies also classified these three genes as variably escaping XCI (Cotton et al. 2013; Balaton et al. 2015), which confirms both our findings and the necessity to account for potential errors in the training list. Although...
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Research: Quantitative analysis of Y-Chromosome gene expression across 36 human tissues
- Alexander K. Godfrey,
- Sahin Naqvi,
- Lukáš Chmátal,
- Joel M. Chick,
- Richard N. Mitchell,
- Steven P. Gygi,
- Helen Skaletsky,
- and David C. Page
Genome Res. June 2020 30: 860-873; Published in Advance May 27, 2020, doi:10.1101/gr.261248.120
...simulation. Three methods were then used to estimate the expression levels of Y-Chromosome genes and their X-linked homologs: (1) Reads were aligned to the using TopHat2 (Kim et al. 2013), and the number of uniquely mapping reads overlapping each gene was counted with featureCounts (Liao et al. 2014) (this...
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Research: The house fly Y Chromosome is young and minimally differentiated from its ancient X Chromosome partner
- Richard P. Meisel,
- Christopher A. Gonzales,
- and Hoang Luu
Genome Res. August 2017 27: 1417-1426; Published in Advance June 15, 2017, doi:10.1101/gr.215509.116
...of the gene encoding the spliceosome-associated protein CWC22 (Sharma et al. 2017), not an ancient gene as would be expected if it were the ancestral male-determining locus of brachycerans. Mdmd has been mapped to the autosomes as well as the Y Chromosome (Sharma et al. 2017), suggesting that the house fly Y...
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Methods: X chromosome cDNA microarray screening identifies a functional PLP2 promoter polymorphism enriched in patients with X-linked mental retardation
- Lilei Zhang,
- Chunfa Jie,
- Cassandra Obie,
- Fatima Abidi,
- Charles E. Schwartz,
- Roger E. Stevenson,
- David Valle,
- and Tao Wang
Genome Res. May 2007 17: 641-648; Published in Advance April 6, 2007, doi:10.1101/gr.5336307
.... , Schroer, R. , Arena, J. , Lubs, H. , Schwartz, C. , Stevenson, R. ( 1996 ) Nonsyndromic X-linked mental retardation: Review and mapping of MRX29 to Xp21 . Clin. Genet. 50 : 176 – 183 . ↵ Herbst, D. , Miller, J. ( 1980 ) Nonspecific X-linked mental retardation II: The frequency in British Columbia . Am. J...
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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
...for a disease with unusual inheritance patterns (Sherman paradox), incomplete penetrance, and strong parent-of-origin effects, paved the way for repeat-centered efforts for many of the other diseases. The localization of the mutant regions of other repeat diseases involved the use of many mapping techniques...
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Research: Evolutionary conservation of Y Chromosome ampliconic gene families despite extensive structural variation
- Wesley A. Brashear,
- Terje Raudsepp,
- and William J. Murphy
Genome Res. December 2018 28: 1841-1851; Published in Advance October 31, 2018, doi:10.1101/gr.237586.118
...greater than 30 were kept and represented those mate pairs most likely to be derived from the Y Chromosome.Sequenced Illumina libraries were trimmed using TrimGalore!, a wrapper tool around Cutadapt (Martin 2011), and were assessed for quality using FastQC. Trimmed libraries were mapped to the Escherichia...

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