Deborah A. Nickerson

Cross-cohort analysis of expression and splicing quantitative trait loci in TOPMed

The paper analyzes expression and splicing quantitative trait loci (e/sQTL) across multiple tissues in the TOPMed dataset and finds that secondary e/sQTL signals are still discoverable, with many GWAS signals colocalizing with these e/sQTL.

The functional impact of rare variation across the regulatory cascade

The paper identifies impactful rare variants by integrating multi-omic data from MESA, showing that combining expression and protein data increases the detection of rare stop and frameshift variants.

Structural variation across 138,134 samples in the TOPMed consortium

The paper presents a comprehensive catalog of structural variants across 138,134 individuals, identifying novel variants and their associations with cardio-metabolic and hematologic traits.

Precision medicine for developmental and epileptic encephalopathies in Africa: strategies for a resource-limited setting.

The paper identifies genetic variants in South African children with developmental and epileptic encephalopathies and proposes a 'Think-Genetics' strategy for early genetic diagnosis in resource-limited settings.

Whole genome sequence analysis of blood lipid levels in >66,000 individuals

The paper performs whole genome sequence analysis of plasma lipid levels in 66,329 individuals, identifying new lipid-associated alleles, including rare non-coding variants.

Genetic interactions drive heterogeneity in causal variant effect sizes for gene expression and complex traits

The paper tests for genetic interactions affecting causal variant effect sizes in gene expression and LDL-C across European and African American populations, finding significant evidence in gene expression but not LDL-C.

Whole genome sequencing as an investigational device for return of hereditary disease risk and pharmacogenomic results as part of the All of Us Research Program

The paper describes the process of obtaining an FDA IDE for returning genomic results via WGS in the All of Us Research Program and presents validation results.

Recovery of trait heritability from whole genome sequence data

The paper estimates heritability for height and BMI using whole-genome sequence data and finds that rare variants contribute significantly to the missing heritability.

Centers for Mendelian Genomics: A decade of facilitating gene discovery

The paper describes the role of the Centers for Mendelian Genomics in advancing gene discovery through data sharing, collaboration, and resource development over the past decade.

Whole genome sequencing identifies common and rare structural variants contributing to hematologic traits in the NHLBI TOPMed program

SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing

SwabExpress is a simplified COVID-19 testing protocol that eliminates the need for transport media and nucleic acid extraction, achieving high sensitivity and specificity.

Benchmarking Association Analyses of Continuous Exposures with RNA-seq in Observational Studies

The paper benchmarks RNA-seq association analyses for continuous exposures using DESeq2, edgeR, limma, and linear regression, finding linear regression methods are faster and better at controlling false detections.

Targeted long-read sequencing resolves complex structural variants and identifies missing disease-causing variants

This paper introduces targeted long-read sequencing to identify complex structural variants and disease-causing mutations missed by conventional methods, improving diagnostic accuracy in genetic disorders.

Type 2 and interferon inflammation strongly regulate SARS-CoV-2 related gene expression in the airway epithelium

The paper identifies eQTLs for ACE2 and TMPRSS2 in children's airway transcriptomes and links their expression to T2 inflammation and interferon responses, influencing SARS-CoV-2 infectivity.

Mutations in MYLPF cause a novel segmental amyoplasia that manifests as distal arthrogryposis

The paper identifies mutations in MYLPF causing segmental amyoplasia with distal arthrogryposis, showing both dominant and recessive inheritance patterns and linking MYLPF impairment to muscle degeneration.

De novo mutations across 1,465 diverse genomes reveal novel mutational insights and reductions in the Amish founder population.

The paper analyzes de novo mutations in 1,465 genomes to show similar mutation rates across ancestries but reduced rates in the Amish population, with environmental factors possibly influencing mutation rates.

ARMC9 and TOGARAM1 define a Joubert syndrome-associated protein module that regulates axonemal post-translational modifications and cilium stability

This study identifies a JBTS-associated protein module involving ARMC9 and TOGARAM1 that regulates ciliary stability and post-translational modifications.

Loss of function, missense, and intronic variants in NOTCH1 confer different risks for left ventricular outflow tract obstructive heart defects in two European cohorts

The paper quantifies the risk of left ventricular outflow tract obstructive heart defects (LVOTO) from different NOTCH1 variants in two European cohorts, identifying significant intronic variants and loss-of-function variants as risk factors.

Narrow-sense heritability estimation of complex traits using identity-by-descent information.

This paper estimates narrow-sense heritability using identity-by-descent information in unrelated individuals and finds that IBD-based methods can capture rare variant contributions but are affected by stratification.

Genetic analysis of de novo variants reveals sex differences in complex and isolated congenital diaphragmatic hernia and indicates MYRF as a candidate gene

The paper analyzes de novo variants in congenital diaphragmatic hernia cases to identify sex differences and a new candidate gene MYRF.

Survival Beyond the Perinatal Period Expands the Phenotypes Caused by Mutations in GLE1

The paper reports two individuals with GLE1 mutations surviving beyond the perinatal period, expanding the phenotype of LAAHD to include childhood survival.

Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome

The paper designs a genotyping array (ADPC) for African-specific genetic variation using whole genome sequences from the CAAPA consortium, improving GWAS for African ancestry populations.