Brandy McNulty
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View article: Long-read sequencing resolves the clinically relevant<i>CYP21A2</i>locus, supporting a new clinical test for Congenital Adrenal Hyperplasia
Long-read sequencing resolves the clinically relevant<i>CYP21A2</i>locus, supporting a new clinical test for Congenital Adrenal Hyperplasia Open
Congenital Adrenal Hyperplasia (CAH), one of the most common inherited disorders, is caused by defects in adrenal steroidogenesis. It is potentially lethal if untreated and is associated with multiple comorbidities, including fertility iss…
View article: Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
Gapless assembly of complete human and plant chromosomes using only nanopore sequencing Open
The combination of ultra-long (UL) Oxford Nanopore Technologies (ONT) sequencing reads with long, accurate Pacific Bioscience (PacBio) High Fidelity (HiFi) reads has enabled the completion of a human genome and spurred similar efforts to c…
View article: Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair
Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair Open
The Genome in a Bottle Consortium (GIAB), hosted by the National Institute of Standards and Technology (NIST), is developing new matched tumor-normal samples, the first to be explicitly consented for public dissemination of genomic data an…
View article: Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection
Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection Open
More than 50% of families with suspected rare monogenic diseases remain unsolved after whole genome analysis by short read sequencing (SRS). Long-read sequencing (LRS) could help bridge this diagnostic gap by capturing variants inaccessibl…
View article: DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies
DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies Open
Somatic variant detection is an integral part of cancer genomics analysis. While most methods have focused on short-read sequencing, long-read technologies now offer potential advantages in terms of repeat mapping and variant phasing. We p…
View article: Phased nanopore assembly with Shasta and modular graph phasing with GFAse
Phased nanopore assembly with Shasta and modular graph phasing with GFAse Open
Reference-free genome phasing is vital for understanding allele inheritance and the impact of single-molecule DNA variation on phenotypes. To achieve thorough phasing across homozygous or repetitive regions of the genome, long-read sequenc…
View article: Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads
Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads Open
Most current studies rely on short-read sequencing to detect somatic structural variation (SV) in cancer genomes. Long-read sequencing offers the advantage of better mappability and long-range phasing, which results in substantial improvem…
View article: Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
Gapless assembly of complete human and plant chromosomes using only nanopore sequencing Open
The combination of ultra-long Oxford Nanopore (ONT) sequencing reads with long, accurate PacBio HiFi reads has enabled the completion of a human genome and spurred similar efforts to complete the genomes of many other species. However, thi…
View article: P821: Long-read sequencing resolves CYP21A2 alleles in congenital adrenal hyperplasia*
P821: Long-read sequencing resolves CYP21A2 alleles in congenital adrenal hyperplasia* Open
We sought to evaluate clinical utility of long-read sequencing (LRS) de novo assemblies and optical genome mapping (OGM) in a research clinical setting for rare disease diagnosis. We focused on regions of the genome of critical importance …
View article: Local read haplotagging enables accurate long-read small variant calling
Local read haplotagging enables accurate long-read small variant calling Open
Long-read sequencing technology has enabled variant detection in difficult-to-map regions of the genome and enabled rapid genetic diagnosis in clinical settings. Rapidly evolving third-generation sequencing platforms like Pacific Bioscienc…
View article: Preliminary assemblies of the three-generational pedigree of African-American ancestry
Preliminary assemblies of the three-generational pedigree of African-American ancestry Open
Monika Cechova1, Sergey Koren2, Julian K. Lucas1, Rebecca Serra Mari3, Mobin Asri1, David Porubsky4, Jordan M. Eizenga1, Brandy McNulty1, Andrey Bzikadze5, Christopher Markovic6, Tamara Potapova7, Jennifer L. Gerton7, Pavel A. Pevzner8, Ev…
View article: Preliminary assemblies of the three-generational pedigree of African-American ancestry
Preliminary assemblies of the three-generational pedigree of African-American ancestry Open
Monika Cechova1, Sergey Koren2, Julian K. Lucas1, Rebecca Serra Mari3, Mobin Asri1, David Porubsky4, Jordan M. Eizenga1, Brandy McNulty1, Andrey Bzikadze5, Christopher Markovic6, Tamara Potapova7, Jennifer L. Gerton7, Pavel A. Pevzner8, Ev…
View article: Phased nanopore assembly with Shasta and modular graph phasing with GFAse
Phased nanopore assembly with Shasta and modular graph phasing with GFAse Open
As a step towards simplifying and reducing the cost of haplotype resolved de novo assembly, we describe new methods for accurately phasing nanopore data with the Shasta genome assembler and a modular tool for extending phasing to the chrom…
View article: The complete sequence of a human Y chromosome
The complete sequence of a human Y chromosome Open
The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure including long palindromes, tandem repeats, and segmental duplications 1–3 . As a result, more than half of the Y chromo…