Searching journal content for articles similar to Laricchia et al. 32 (3): 569.

Displaying results 1-9 of 9

For checked items

view abstracts
download to citation manager

Select this article
Review: A systematic review on the biochemical threshold of mitochondrial genetic variants
- Karan K. Smith,
- Jesse D. Moreira,
- Callum R. Wilson,
- June O. Padera,
- Ashlee N. Lamason,
- Liying Xue,
- Deepa M. Gopal,
- David B. Flynn,
- and Jessica L. Fetterman
Genome Res. March 2024 34: 341-365; Published in Advance April 16, 2024, doi:10.1101/gr.278200.123
...mitochondrial function across a wide range of VAFs in order to sufficiently identify the biochemical threshold for pathogenic mtDNA variants in protein-encoding genes.MethodsA subset of relevant articles identified before the literature search was used to obtain controlled vocabulary terms (Majander et al. 1991...
OPEN ACCESS ARTICLE
Select this article
Method: Estimation of intrafamilial DNA contamination in family trio genome sequencing using deviation from Mendelian inheritance
- Christopher J. Yoon,
- Su Yeon Kim,
- Chang Hyun Nam,
- Junehawk Lee,
- Jung Woo Park,
- Jihyeob Mun,
- Seongyeol Park,
- Soyoung Lee,
- Boram Yi,
- Kyoung Il Min,
- Brian Wiley,
- Kelly L. Bolton,
- Jeong Ho Lee,
- Eunjoon Kim,
- Hee Jeong Yoo,
- Jong Kwan Jun,
- Ji Seon Choi,
- Malachi Griffith,
- Obi L. Griffith,
- and Young Seok Ju
Genome Res. November/December 2022 32: 2134-2144; Published in Advance December 6, 2022, doi:10.1101/gr.276794.122
...be calculated, Selection of common SNPs from gnomAD databaseWe selected common SNPs from the gnomAD database (Karczewski et al. 2020). For GRCh37 we used gnomAD v2, and for GRCh38, we used gnomAD v3. The raw VCF files were downloaded, and common biallelic SNPs with a population allele frequency (AF) greater...
OPEN ACCESS ARTICLE
Select this article
Method: De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data
- Arthur Dondi,
- Nico Borgsmüller,
- Pedro F. Ferreira,
- Brian J. Haas,
- Francis Jacob,
- Viola Heinzelmann-Schwarz,
- Tumor Profiler Consortium,
- and Niko Beerenwinkel
Genome Res. April 2025 35: 900-913; Published in Advance March 19, 2025, doi:10.1101/gr.279281.124
...Som tests if, when ignoring the reads harboring candidate allele mutation reads, other nonreference allele counts at the locus are significantly higher than expected given the background error rate (beta-binomial test, significance threshold 0.05). Loci (3) within homopolymers, (4) present in the gnomAD...
OPEN ACCESS ARTICLE
Select this article
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
...) and performed stratified logistic regression modeling (Supplemental Table S4). We explored multiple predictors, including gene age (T; mya), gene length (Lg) or protein length (L), gene-wise burden of deleterious DNVs (D) from 46,612 trios (Wang et al. 2022), and rare variant burden (R) based on gnomAD s...
OPEN ACCESS ARTICLE
Select this article
Method: A complete pedigree-based graph workflow for rare candidate variant analysis
- Charles Markello,
- Charles Huang,
- Alex Rodriguez,
- Andrew Carroll,
- Pi-Chuan Chang,
- Jordan Eizenga,
- Thomas Markello,
- David Haussler,
- and Benedict Paten
Genome Res. May 2022 32: 893-903; Published in Advance April 28, 2022, doi:10.1101/gr.276387.121
...to use gnomAD v3.1, which has incorporated a larger proportion of samples producing more accurate and exhaustive population allele frequencies (Karczewski et al. 2020). The maximum minor allele frequency (MAXMAF) calculation implemented in the population/deleterious-backed variant filtration module...
Select this article
Method: Three-dimensional missense tolerance ratio analysis
- Riley E. Perszyk,
- Anders S. Kristensen,
- Polina Lyuboslavsky,
- and Stephen F. Traynelis
Genome Res. August 2021 31: 1447-1461; Published in Advance July 22, 2021, doi:10.1101/gr.275528.121
...residues (MTR = 0) that corresponds to the SYTANLAAF motif, which is conserved in all glutamate receptors (Traynelis et al. 2010). To understand what this score captures, one can observe the occurrence of the gnomAD variants (version v2.1.1) (Karczewski et al. 2020) throughout the gene sequence (Fig. 1B...
Select this article
Research: Unraveling undiagnosed rare disease cases by HiFi long-read genome sequencing
- Wouter Steyaert,
- Lydia Sagath,
- German Demidov,
- Vicente A. Yépez,
- Anna Esteve-Codina,
- Julien Gagneur,
- Kornelia Ellwanger,
- Ronny Derks,
- Marjan Weiss,
- Amber den Ouden,
- Simone van den Heuvel,
- Hilde Swinkels,
- Nick Zomer,
- Marloes Steehouwer,
- Luke O'Gorman,
- Galuh Astuti,
- Kornelia Neveling,
- Rebecca Schüle,
- Jishu Xu,
- Matthis Synofzik,
- Danique Beijer,
- Holger Hengel,
- Ludger Schöls,
- Kristl G. Claeys,
- Jonathan Baets,
- Liedewei Van de Vondel,
- Alessandra Ferlini,
- Rita Selvatici,
- Heba Morsy,
- Marwa Saeed Abd Elmaksoud,
- Volker Straub,
- Juliane Müller,
- Veronica Pini,
- Luke Perry,
- Anna Sarkozy,
- Irina Zaharieva,
- Francesco Muntoni,
- Enrico Bugiardini,
- Kiran Polavarapu,
- Rita Horvath,
- Evan Reid,
- Hanns Lochmüller,
- Marco Spinazzi,
- Marco Savarese,
- Solve-RD DITF-ITHACA, Solve-RD DITF-Euro-NMD, Solve-RD DITF-RND, Solve-RD DITF-EpiCARE,
- Leslie Matalonga,
- Steven Laurie,
- Han G. Brunner,
- Holm Graessner,
- Sergi Beltran,
- Stephan Ossowski,
- Lisenka E.L.M. Vissers,
- Christian Gilissen,
- Alexander Hoischen,
- and on behalf of the Solve-RD consortium
Genome Res. April 2025 35: 755-768; Published in Advance March 26, 2025, doi:10.1101/gr.279414.124
...to the proteolytic pathway of aberrant proteins and/or proteins with high turnover rates in the ubiquitin-proteasome system (UPS). Variants in PSMA3 have not previously been linked to disease and no exonic PSMA3 deletions have been described in gnomAD SVs v4.1.0. However, variants in genes contributing to the UPS...
OPEN ACCESS ARTICLE
Select this article
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
...of alleles in gnomAD have nonpathogenic reference motif (AAAAT) expansions >30 repeats for SCA31 and SCA37 (out of 18,511 individuals). SR-GS methods are mostly unable to detect cases where a pathogenic RE is embedded deep within nonpathogenic motifs due to short DNA fragment libraries and reliance...
Select this article
Resource: A platform for curated products from novel open reading frames prompts reinterpretation of disease variants
- Matthew D.C. Neville,
- Robin Kohze,
- Chaitanya Erady,
- Narendra Meena,
- Matthew Hayden,
- David N. Cooper,
- Matthew Mort,
- and Sudhakaran Prabakaran
Genome Res. February 2021 31: 327-336; Published in Advance January 19, 2021, doi:10.1101/gr.263202.120
...in the following analyses by examining specific nORF variant classes.Mutability-adjusted proportion of singletonsTo examine the potential functional importance of nORFs separately from canonical CDS, we drew on variant frequencies from the Genome Aggregation Database (gnomAD) data sets, made up of 125,748 exome...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Laricchia et al. 32 (3): 569.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: