Megan Shand

Exploring penetrance of clinically relevant variants in over 800,000 humans from the Genome Aggregation Database

Sanna Gudmundsson, Moriel Singer‐Berk, Sarah L. Stenton, Julia K. Goodrich et autres

Incomplete penetrance, or absence of disease phenotype in an individual with a disease-associated variant, is a major challenge in variant interpretation. Studying individuals with apparent incomplete penetrance can shed light on underlying drivers of altered phenotype penetrance. Here, we investigate clinically relevant …

us, se, Kenya, mx, gb, fr, ca, it, es, il, cr, hk, ie, fi, de, ee, au, be, pe (code pays fourni par la source)

Blended Length Genome Sequencing (blend-seq): Combining Short Reads with Low-Coverage Long Reads to Maximize Variant Discovery

Ricky Magner, Fabio Cunial, Sumit Basu, Ron Paulsen et autres

We introduce blend-seq, a method for combining data from traditional short-read sequencing pipelines with low-coverage long reads, with the goal of substantially improving variant discovery for single samples without the full cost of high-coverage long reads. We demonstrate that with only 4x …

us (code pays fourni par la source)

Author Correction: A genomic mutational constraint map using variation in 76,156 human genomes

Siwei Chen, Laurent C. Francioli, Julia K. Goodrich, Ryan L. Collins et autres

us, jp, mx, gb, it, il, fr, cr, hk, ca, es, de, ee, au, fi (code pays fourni par la source)

A genomic mutational constraint map using variation in 76,156 human genomes

Siwei Chen, Laurent C. Francioli, Julia K. Goodrich, Ryan L. Collins et autres

us, jp, mx, gb, it, il, fr, cr, hk, ca, es, de, ee, au, fi (code pays fourni par la source)

Inferring compound heterozygosity from large-scale exome sequencing data

Michael H. Guo, Laurent C. Francioli, Sarah L. Stenton, Julia K. Goodrich et autres

us, mx, gb, it, il, fr, cr, hk, fi, es, de, ee, au, se, kr (code pays fourni par la source)

Cover Image, Volume 49, Issue 4

Abrar Alhindi, Megan Shand, Hannah Smith, Ana S. Leite et autres

The cover image is based on the Original Article Neuromuscular junction denervation and terminal Schwann cell loss in the hTDP-43 overexpression mouse model of amyotrophic lateral sclerosis by Abrar Alhindi et al., https://doi.org/10.1111/nan.12925. Image Credit: Abrar Alhindi and Helena Chaytow.

Neuromuscular junction denervation and terminal Schwann cell loss in the hTDP‐43 overexpression mouse model of amyotrophic lateral sclerosis

Abrar Alhindi, Megan Shand, Hannah Smith, Ana S. Leite et autres

Abstract Aims Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with complex aetiology. Despite evidence of neuromuscular junction (NMJ) denervation and ‘dying‐back’ pathology in models of SOD1‐dependent ALS, evidence in other genetic forms of ALS is limited by a lack of …

gb, sa, br (code pays fourni par la source)

Cost-efficient whole genome-sequencing using novel mostly natural sequencing-by-synthesis chemistry and open fluidics platform

Gilad Almogy, Mark Pratt, Florian C. Oberstrass, Linda Lee et autres

Abstract We introduce a massively parallel novel sequencing platform that combines an open flow cell design on a circular wafer with a large surface area and mostly natural nucleotides that allow optical end-point detection without reversible terminators. This platform enables sequencing billions …

us (code pays fourni par la source)

The ‘Tea Test’ - a mobile phone based spectrophotometer protocol to introduce biochemical methods independent of the laboratory

Katharine Hubbard, Marlena Birycka, Maisie-Elizabeth Britton, Joseph Coates et autres

Providing hands-on practical education without access to laboratories during the Covid-19 pandemic has required creativity and innovation. In this paper, co-authored by academic staff and students, we describe an at-home mobile phone-based ‘spectrophotometer’ experiment used in an introductory undergraduate biology course. Using …

gb (code pays fourni par la source)

Mitochondrial DNA variation across 56,434 individuals in gnomAD

Kristen M. Laricchia, Nicole J. Lake, Nicholas A. Watts, Megan Shand et autres

Genomic databases of allele frequency are extremely helpful for evaluating clinical variants of unknown significance; however, until now, databases such as the Genome Aggregation Database (gnomAD) have focused on nuclear DNA and have ignored the mitochondrial genome (mtDNA). Here, we present a …

us, au (code pays fourni par la source)

Mitochondrial DNA variation across 56,434 individuals in gnomAD

Kristen M. Laricchia, Nicole J. Lake, Nicholas A. Watts, Megan Shand et autres

ABSTRACT Databases of allele frequency are extremely helpful for evaluating clinical variants of unknown significance; however, until now, genetic databases such as the Genome Aggregation Database (gnomAD) have ignored the mitochondrial genome (mtDNA). Here we present a pipeline to call mtDNA variants …

us, au (code pays fourni par la source)

A validated lineage-derived somatic truth data set enables benchmarking in cancer genome analysis

Megan Shand, José Soto, Lee Lichtenstein, David Benjamin et autres

Existing cancer benchmark data sets for human sequencing data use germline variants, synthetic methods, or expensive validations, none of which are satisfactory for providing a large collection of true somatic variation across a whole genome. Here we propose a data set, Lineage …

us (code pays fourni par la source)