Topic 97

variants sequencing variant genome genomics whole genomic genetic mutations nucleotide genetics variation exome allele snps wgs population samples individuals snp somatic mutation cancer dna rare copy calling genes data alleles identified clinical detection pathogenic deletions genomes genotyping bioinformatics mutational frequency number sequence coverage developed polymorphisms sequenced calls single gene svs read interpretation cnvs reference identification novo insertions coding germline snvs cohort high genotype frequencies diagnosis de detected generation missense homozygous sv accuracy recessive large indels pipeline allelic cases autosomal structural likely inherited false populations used panel variations haplotype cnv accurate novel identify patients genotypes next detect all 10 polymorphic pathogenicity

280 items. Top items listed below.

Insights into dispersed duplications and complex structural mutations from whole genome sequencing 706 families 97 19 4

MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data 97 25 9 4

Mobile Element Insertions and Associated Structural Variants in Longitudinal Breast Cancer Samples 97 9

Accuracy and efficiency of germline variant calling pipelines for human genome data 97 4

A genome-wide case-only test for the detection of digenic inheritance in human exomes 145 19 4

Detecting oncogenic selection through biased allele retention in The Cancer Genome Atlas 97 7 5 4

Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs 25 19 9 4

StrVCTVRE: A supervised learning method to predict the pathogenicity of human structural variants. 97 4

Next generation cytogenetics: comprehensive assessment of 48 leukemia genomes by genome imaging 97 25 9 4

Whole Genome Sequences of Aedes aegypti (Linn.) Field Isolates from Southern India 48 25 9 5 4

Integrative analysis of mutated genes and mutational processes reveals seven colorectal cancer subtypes 97 9 4

The landscape of interactions between cancer polygenic risk scores and somatic alterations in cancer cells 97 9 4

Exploring the effects of genetic variation on gene regulation in cancer in the context of 3D genome structure 89 19 9 4

Unbalanced Sample Size Introduces Spurious Correlations to Genome-wide Heterozygosity Analyses 145 19 4

De novo structural mutation rates and gamete-of-origin biases revealed through genome sequencing of 2,396 families 97 21 5

Evolution and genomic signatures of spontaneous somatic mutation in Drosophila intestinal stem cells 97 9

A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism. 97 25 9 4

Bacterial single-cell genomics enables phylogenetic analysis and reveals population structures from in vitro evolutionary studies 107 52 12 9 5 4

Expression changes confirm genomic variants predicted to result in allele-specific, alternative mRNA splicing 97 9 4

GREEN-DB: a framework for the annotation and prioritization of non-coding regulatory variants in whole-genome sequencing 97 9 4

Controlling for Human Population Stratification in Rare Variant Association Studies 145 123 19 4

Genomic loci susceptible to systematic sequencing bias in clinical whole genomes 97 25 4

Variant Phasing and Haplotypic Expression from Single-molecule Long-read Sequencing in Maize 97 25 9 4

Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph 97 25 4

Efficient phasing and imputation of low-coverage sequencing data using large reference panels 145 97 4

Probabilistic Approach to Understand Errors in Sequencing and its based Applications 145 4

Transcript expression-aware annotation improves rare variant discovery and interpretation 97 9 4

Effective variant filtering and expected candidate variant yield in studies of rare human disease 165 97 13 4

Expectations and blind spots for structural variation detection from short-read alignment and long-read assembly 25 7 4

MapCaller - An integrated and efficient tool for short-read mapping and variant calling using high-throughput sequenced data 13 4

Detection of complex genetic architecture using two-locus population differentiation: modeling epistasis 19 9 4

The consequences of variant calling decisions in secondary analyses of cancer sequencing data 97 4

Improving the coverage of credible sets in Bayesian genetic fine-mapping 19 4

Recessive deleterious variation has a limited impact on signals of adaptive introgression in human populations 21 5 4

A genome-wide scan for candidate lethal variants in Thoroughbred horses. 97 9 5

Amplification-free long read sequencing reveals unforeseen CRISPR-Cas9 off-target activity 25 4

Intra-host Variation and Evolutionary Dynamics of SARS-CoV-2 Population in COVID-19 Patients 37 1

Polymorphic mobile element insertions contribute to gene expression and alternative splicing in human tissues 97 9

Unique K-mer sequences for validating cancer-related substitution, insertion and deletion mutations 97 4

Whole genome sequencing of cell-free DNA yields genome-wide read distribution patterns to track tissue of origin in cancer patients 97 9 4

An evaluation of pool-sequencing transcriptome-based exon capture for population genomics in non-model species 97 25 4

Detecting copy number alterations in RNA-Seq using SuperFreq 97 13 4

De Novo Mutation in an Enhancer of EBF3 in simplex autism 97 9

Allele-specific alternative splicing in human tissues 19 9 4

Evolutionarily conserved non-protein-coding regions in the chicken genome harbor functionally important variation 97 19 9 5

Vector and cell-culture passaging of dengue clinical samples for virus isolation and amplification does not significantly change genome consensus or frequencies of intra-host viral variants 97 37 5

Predicting evolutionary change at the DNA level in a natural Mimulus population 21 5 4

Enhanced specificity of high sensitivity somatic variant profiling in cell-free DNA via paired normal sequencing: design, validation, and clinical experience of the MSK-ACCESS liquid biopsy assay 173 97 14 9 4

Whole-genome sequencing of 1,171 elderly admixed individuals from the largest Latin American metropolis (Sao Paulo, Brazil) 97 19 4

BAdabouM: a genomic structural variations discovery tool for polymorphism analyses 97 25 4

Pathway Analysis within Multiple Human Ancestries Reveals Novel Signals for Epistasis in Complex Traits 19 4

The extent and impact of variation in ADME genes in sub-Saharan African populations 97 5 4

A novel framework for characterizing genomic haplotype diversity in the human immunoglobulin heavy chain locus 97 25 4

TADA - a Machine Learning Tool for Functional Annotation based Prioritisation of Putative Pathogenic CNVs 97 26 4

Integrating Genomic Correlation Structure Improves Copy Number Variations Detection 145 4

Tumor-specific changes in Kaposi sarcoma-associated herpesvirus genomes in Ugandan adults with Kaposi sarcoma 97 25 9 5

How Array Design Affects SNP Ascertainment Bias 97 19 5 4

MHC*IMP - Imputation of Alleles for Genes in the Major Histocompatibility Complex 97 25 19 4

Population matched (PM) germline allelic variants of immunoglobulin (IG) loci: New pmIG database to better understand IG repertoire and selection processes in disease and vaccination 97 4

Efficient and Flexible Integration of Variant Characteristics in Rare Variant Association Studies Using Integrated Nested Laplace Approximation 145 13 4

A cautionary note on the use of haplotype callers in Phylogenomics 97 25 5 4

In silico candidate variant and gene identification using inbred mouse strains 97 19 4

Whole genome analysis of four Bangladeshi individuals 97 9 4

Systematic evaluation of genome sequencing as a first-tier diagnostic test for prenatal and pediatric disorders 97 19 15 9 4

Assessing in vivo mutation frequencies and creating a high-resolution genome-wide map of fitness costs of Hepatitis C virus 21 5

nanotatoR: A tool for enhanced annotation of genomic structural variants 97 25 4

A comprehensive benchmarking of WGS-based structural variant callers 97 4

Adapting genotyping-by-sequencing and variant calling for heterogeneous stock rats 145 97 4

Dissecting Autism Genetic Risk Using Single-cell RNA-seq Data 9 4

Utility of a high-resolution mouse single nucleotide polymorphism microarray assessed for rodent comparative genomics 97 40 5 4

SVJedi: Genotyping structural variations with long reads 25 13 4

Landscape of allele-specific transcription factor binding in the human genome 31 9 4

PopDel identifies medium-size deletions jointly in tens of thousands of genomes 97 25 4

A Genome-based Model to Predict the Virulence of Pseudomonas aeruginosa Isolates 26 4

Enrichment of genomic variation in pathways linked to autism 9 4

Long-read sequencing resolves structural variants in SERPINC1 causing antithrombin deficiency and identifies a complex rearrangement and a retrotransposon insertion not characterized by routine diagnostic methods 97 25 9 4

ATAV: a comprehensive platform for population-scale genomic analyses 165 62 13 4

A domestic cat whole exome sequencing resource for trait discovery 97 25 19 9 4

Multi-tissue transcriptome-wide association studies 19 4

The genomic and epigenomic evolutionary history of papillary renal cell carcinomas 97 14 9 5

Discovering the drivers of clonal hematopoiesis 97 9 4

Harnessing population-specific protein truncating variants to improve the annotation of loss-of-function alleles 97 4

Using deep mutational scanning to benchmark variant effect predictors and identify disease mutations 97 4

Controlling for off-target genetic effects using polygenic scores improves the power of genome-wide association studies 19 4

STAMP: a multiplex sequencing method for simultaneous evaluation of mitochondrial DNA heteroplasmies and content 97 25 4

A deep learning framework for characterization of genotype data 26 4

Whole-organism mapping of the genetics of gene expression at cellular resolution 19 9 4

Long-read genome sequencing for the diagnosis of neurodevelopmental disorders 25 4

Identifying non-identical-by-descent rare variants in population-scale whole genome sequencing data 145 83 21 4

GeneBreaker: Variant simulation to improve the diagnosis of Mendelian rare genetic diseases 97 4

Taking the next-gen step: comprehensive antimicrobial resistance detection from Burkholderia pseudomallei 97 25 12 4

Absent from DNA and protein: genomic characterization of nullomers and nullpeptides across functional categories and evolution 121 97 40 21 5

Using high-throughput phenotypes to enable genomic selection by inferring genotypes 145 53 19 4

One is not enough: on the effects of reference genome for the mapping and subsequent analyses of short-reads 25 5 4

Reprogramming enriches for somatic cell clones with small scale mutations in cancer-associated genes 97 14 9

Model-based analysis of polymorphisms in an enhancer reveals cis-regulatory mechanisms 134 112 4

Hybridization capture and low-coverage SNP profiling for extended kinship analysis and forensic identification of historical remains 97 25 4

Burden analysis of missense variants in 1,330 disease-associated genes on 3D provides insights into the mutation effects 97 9

Optimizing Sequencing Resources in Genotyped Livestock Populations Using Linear Programming 145 97 4

Polygenic risk score based on weight gain trajectories is a strong predictor of childhood obesity 19 4