Samantha Zarate

This study quantifies cancer risk and penetrance in CHEK2 heterozygotes using genomic data from two large biobanks, finding increased risks for several cancers and younger age of onset.

The paper presents the complete sequence of a human Y chromosome, correcting errors in the GRCh38 reference and adding over 30 million base pairs.

The paper investigates how excluding the X chromosome in human genomics affects variant calling and finds that using a sex chromosome-aware reference genome allows reliable variant calls across the entire X chromosome.

This paper expands genome benchmarking to include difficult-to-map regions using linked and long reads, identifying more false negatives in variant calling.

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

The T2T-CHM13 reference genome improves read mapping and variant calling across diverse samples, reducing false positives and enabling novel variant discovery.

The paper describes AnVIL, a cloud-based platform that enables genomic data analysis without data transfer, improving security, scalability, and collaboration.

The paper develops a diploid assembly-based benchmark for variants in the MHC region using HG002 data, identifying 21496 small variants with high concordance to clinical HLA types.

The paper catalogs structural variants across 19,652 genomes and identifies their associations with proteomic measurements and disease phenotypes.

Parliament2 combines multiple structural variant callers to improve accuracy and speed, offering a Docker-based solution for efficient variant calling.