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Research: Pedigree-based estimation of human mobile element retrotransposition rates
- Julie Feusier,
- W. Scott Watkins,
- Jainy Thomas,
- Andrew Farrell,
- David J. Witherspoon,
- Lisa Baird,
- Hongseok Ha,
- Jinchuan Xing,
- and Lynn B. Jorde
Genome Res. October 2019 29: 1567-1577; doi:10.1101/gr.247965.118
...retrotransposition activity (Goodier 2016). Future studies of retrotransposition in large pedigree-based cohorts may help to elucidate variants and genetic factors involved in the regulation of L1-mediated retrotransposition activity.MethodsCEPH individualsBlood-derived DNA samples from 599 individuals, including...
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Method: Phased nanopore assembly with Shasta and modular graph phasing with GFAse
- Ryan Lorig-Roach,
- Melissa Meredith,
- Jean Monlong,
- Miten Jain,
- Hugh E. Olsen,
- Brandy McNulty,
- David Porubsky,
- Tessa G. Montague,
- Julian K. Lucas,
- Chris Condon,
- Jordan M. Eizenga,
- Sissel Juul,
- Sean K. McKenzie,
- Sara E. Simmonds,
- Jimin Park,
- Mobin Asri,
- Sergey Koren,
- Evan E. Eichler,
- Richard Axel,
- Bruce Martin,
- Paolo Carnevali,
- Karen H. Miga,
- and Benedict Paten
Genome Res. March 2024 34: 454-468; Published in Advance April 16, 2024, doi:10.1101/gr.278268.123
..., while also not requiring parental data.The approach described here leverages the assembly graph to phase and extend partial haplotypes. In this scheme, variants are not inferred from the read alignments. Instead, graph topology or sequence homology is used to identify large-scale haplotypic bubbles...
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Method: A pedigree-based prediction model identifies carriers of deleterious de novo mutations in families with Li-Fraumeni syndrome
- Fan Gao,
- Xuedong Pan,
- Elissa B. Dodd-Eaton,
- Carlos Vera Recio,
- Matthew D. Montierth,
- Jasmina Bojadzieva,
- Phuong L. Mai,
- Kristin Zelley,
- Valen E. Johnson,
- Danielle Braun,
- Kim E. Nichols,
- Judy E. Garber,
- Sharon A. Savage,
- Louise C. Strong,
- and Wenyi Wang
Genome Res. August 2020 30: 1170-1180; Published in Advance August 18, 2020, doi:10.1101/gr.249599.119
...is de novo. The de novo probability of interest can be written as the Pr(father is a noncarrier, mother is a noncarrier | child is a mutation carrier, family history). We calculate this probability as a function, g(c, f, m), of pedigree-based carrier probabilities for the child (c), father (f...
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Research: Highly complete long-read genomes reveal pangenomic variation underlying yeast phenotypic diversity
- Cory A. Weller,
- Ilya Andreev,
- Michael J. Chambers,
- Morgan Park,
- NISC Comparative Sequencing Program,
- Joshua S. Bloom,
- and Meru J. Sadhu
Genome Res. May 2023 33: 729-740; Published in Advance May 1, 2023, doi:10.1101/gr.277515.122
...owing to genetic linkage between causal variants and neighboring variants, requiring further study to identify the causal variants. QTLs can be mapped even if the parental sequences are not completely known, if genetic variants linked to the causal variant are genotyped. Complete sequences are desired...
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Research: Small polymorphisms are a source of ancestral bias in structural variant breakpoint placement
- Peter A. Audano and
- Christine R. Beck
Genome Res. January 2024 34: 7-19; Published in Advance January 4, 2024, doi:10.1101/gr.278203.123
...and to address the issues outlined here. However, because rare and somatic variants cannot be captured by graph references, the same challenges must still be addressed.Although this paper focuses on variants not anchored in complex repeats, some of the most impactful biology is emerging from complex loci...
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Method: Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing
- Yuhong Sun,
- Zhanwen Cheng,
- Xiang Li,
- Qing Yang,
- Bixi Zhao,
- Ziqi Wu,
- and Yu Xia
Genome Res. April 2023 33: 612-621; Published in Advance April 11, 2023, doi:10.1101/gr.277266.122
...for normal sequencing and the remaining channels for selective sequencing. (C) The bioinformatic workflow for HQ-MAGs retrieval based on data sets derived from nanopore selective sequencing and Illumina sequencing.Here we show our results in applying the metaRUpore protocol to facilitate the recovery of rare...
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Method: Accurate and fast graph-based pangenome annotation and clustering with ggCaller
- Samuel T. Horsfield,
- Gerry Tonkin-Hill,
- Nicholas J. Croucher,
- and John A. Lees
Genome Res. September 2023 33: 1622-1637; Published in Advance August 24, 2023, doi:10.1101/gr.277733.123
...the open-source software graph-gene-caller (ggCaller). ggCaller combines gene prediction, functional annotation, and clustering into a single workflow using population-wide de Bruijn graphs, removing redundancy in gene annotation and resulting in more accurate gene predictions and orthologue clustering. We...
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Method: Analyzing rare mutations in metagenomes assembled using long and accurate reads
- Marcus W. Fedarko,
- Mikhail Kolmogorov,
- and Pavel A. Pevzner
Genome Res. November/December 2022 32: 2119-2133; Published in Advance November 23, 2022, doi:10.1101/gr.276917.122
...), enabling “complete metagenomics” studies that were nearly impossible to conduct with short reads. In particular, HiFi reads simplify the identification and phasing of mutations in MAGs: It is increasingly feasible to distinguish between positions that are prone to mutations and positions that rarely ever...
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Resource: Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotype
- Julie A. Karl,
- Trent M. Prall,
- Hailey E. Bussan,
- Joshua M. Varghese,
- Aparna Pal,
- Roger W. Wiseman,
- and David H. O'Connor
Genome Res. March 2023 33: 448-462; Published in Advance February 28, 2023, doi:10.1101/gr.277429.122
...many of these human disease associations have been attributed to specific MHC-I and MHC-II alleles, linkage disequilibrium in this gene-dense region makes the identification of specific causative variants for disease phenotypes extremely challenging. Non–immune system loci that make up the majority...
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Research: A naturally occurring variant of MBD4 causes maternal germline hypermutation in primates
- Alexandra M. Stendahl,
- Rashesh Sanghvi,
- Samuel Peterson,
- Karina Ray,
- Ana C. Lima,
- Raheleh Rahbari,
- and Donald F. Conrad
Genome Res. December 2023 33: 2053-2059; Published in Advance November 20, 2023, doi:10.1101/gr.277977.123
...Center, we identified a rhesus macaque with a rare homozygous frameshift mutation in the gene methyl-CpG binding domain 4, DNA glycosylase (MBD4). MBD4 is responsible for the repair of C > T deamination mutations at CpG dinucleotides and has been linked to somatic hypermutation and cancer predisposition...
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