Kendra Hoekzema

Decoding the naked mole-rat genome, telomere to telomere

The paper presents a telomere-to-telomere genome assembly of the naked mole-rat and compares it with a related species to identify gene losses and duplications associated with unique traits.

Long-read sequencing and benchmarking of saliva against blood for genomic variant detection in autism

This study benchmarks saliva-derived DNA against blood for long-read sequencing in autism, showing comparable variant detection despite nonhuman DNA contamination.

Structural variants from donor-specific assemblies affect recurrent chromatin contact divergence in humans

The paper shows that structural variants from donor-specific assemblies influence chromatin contact divergence in humans, with many SVs linked to regulatory contexts and expression variation.

Distinct mechanisms of CNV formation at the human 15q13.3 locus

The paper identifies distinct mechanisms of CNV formation at the human 15q13.3 locus, showing that non-allelic homologous recombination is the primary mechanism, influenced by inversion polymorphisms and population-specific susceptibility.

Sequence and epigenetic characterization of chromosome 21 centromeres in a family with recurrent Trisomy 21

The paper characterizes chromosome 21 centromeres in a family with recurrent Trisomy 21, identifying a diffuse hypomethylation pattern linked to maternal age-related risk.

Androgens mediate sexual dimorphism in Pilarowski-Bjornsson Syndrome

The paper investigates sex-specific penetrance in PILBOS, showing male overrepresentation and androgen-mediated sexual dimorphism through genetic and mouse model studies.

A high-resolution human pangenome structural variant resource for improved disease association

The paper constructs a high-resolution human pangenome structural variant resource, identifies disease-associated SVs, and demonstrates its utility in filtering variants from probands and associating SVs with traits in a large cohort.

Pangenome discovery and characterization of human protein-coding duplicated genes

The paper identifies and characterizes human protein-coding duplicated genes using long-read genomic and transcriptomic data, revealing new gene models and constraint patterns.

A comprehensive assessment of tandem repeat genotyping methods for Nanopore long-read genomes

This paper benchmarks 7 TR genotyping tools using Nanopore long-read data, finding that no single tool is best across all metrics, and that sequence-level accuracy is crucial for clinical and population studies.

Human acrocentric chromosome short arm de novo mutation and recombination

The paper investigates mutation and recombination patterns in human acrocentric chromosome short arms using multiple sequencing technologies and a four-generation pedigree.

A global view of human centromere variation and evolution

The paper assembles and characterizes 2,110 human centromeres, revealing novel haplotypes, mobile element insertions, and mutation rate variation across chromosomes.

Complete chromosome 21 centromere sequencing of families with Down syndrome reveals centromere size asymmetry

The paper sequences chromosome 21 centromeres in Down syndrome families, finding extreme size asymmetry in some cases and suggesting it may be a genetic risk factor.

A global map for introgressed structural variation and selection in humans

Long-read phased assemblies from two Papuans plus 47 HPRC genomes map archaic introgressed structural variants, revealing 11 candidate archaic centromeres and 16 candidate adaptive SVs.

A Pan-pangenome illuminates complex structural variation and selection in humans, chimpanzees, and bonobos

This study presents a pan-pangenome of humans, chimpanzees, and bonobos, revealing structural variation, selection patterns, and adaptations related to immunity and malaria resistance.

Rapid centromere turnover and the adaptive radiation of lemurs

The paper analyzes centromere evolution in lemurs using long-read sequencing, finding rapid sequence turnover and distinct centromeric repeats across species.

A family portrait of the genomic factors shaping tandem repeat mutagenesis

This study identifies genomic factors influencing tandem repeat mutagenesis using long-read sequencing in a large family, finding that de novo mutations are more common at longer, uninterrupted, and heterozygous loci.

Population differences of chromosome 22q11.2 duplication structure predispose differentially to microdeletion and inversion.

The paper analyzes chromosome 22q11.2 haplotypes to show how structural variations in specific regions correlate with microdeletion and inversion risks across populations.

MitoScope: a comprehensive mitochondrial genome analysis workflow for long-read sequencing data

MitoScope is a long-read sequencing workflow for mitochondrial genome analysis that improves sensitivity and precision in variant detection and NUMT profiling.

A segmental duplication-mediated deletion leads to neocentromere formation in orangutans

The paper identifies a segmental duplication-mediated deletion causing neocentromere formation in orangutans by analyzing structural and epigenetic variation.

Genetic diversity and regulatory features of human-specific NOTCH2NL duplications

The paper characterizes the genetic diversity and regulatory features of human-specific NOTCH2NL duplications using long-read sequencing and organoid models.

Donor-specific assemblies enhance somatic structural variant detection in complex genomic regions

This study benchmarks donor-specific assemblies for improved detection of somatic structural variants in a melanoma cell line, finding they identify more variants, especially in repeat-rich regions.

Pangenome discovery of missing autism variants

The paper uses long-read sequencing to identify pathogenic variants in autism cases, finding three pathogenic mutations and nine candidate structural variants missed by short-read sequencing.

NPEPPS segmental duplication drives position effect expression of TBC1D3 in the human brain

The paper identifies a segmental duplication that drives position effect expression of TBC1D3 in the human brain, explaining its high structural heterozygosity.

Haplotype-Resolved Genomics Reveals Conserved Chromatin Architecture and Epigenetic Constraints of Human Neocentromeres

The paper investigates how neocentromeres reshape chromatin and identifies conserved features of native centromeres using haplotype-resolved assemblies and multi-omics data.

A telomere-to-telomere map of somatic mutation burden and functional impact in cancer

The paper maps somatic mutation burden and functional impact across the cancer genome using telomere-to-telomere sequencing, revealing novel mutation hotspots and regulatory rewiring mechanisms.

The Platinum Pedigree: A long-read benchmark for genetic variants

The paper creates a long-read benchmark for genetic variants using a large pedigree, improving variant calling performance and introducing new truth sets for tandem repeats and structural variants.

Complex genetic variation in nearly complete human genomes

Hybrid HiFi/ultra-long ONT assemblies of 65 diverse humans yield 130 haplotypes, 1,246 complete centromeres, and a pangenome panel enabling short-read genome inference at median QV 45.

Long-read sequencing of trios reveals increased germline and postzygotic mutation rates in repetitive DNA

The paper uses long-read sequencing to analyze de novo mutations in autism families, finding higher mutation rates in repetitive DNA and a paternal bias in postzygotic mutations.

A familial, telomere-to-telomere reference for human de novo mutation and recombination from a four-generation pedigree

The paper uses a four-generation family to systematically assess de novo mutations and recombination, finding high mutation rates and paternal bias, along with a detailed recombination map.

Complete sequencing of ape genomes

The paper presents haplotype-resolved genomes of six ape species with high accuracy and provides comparative analyses to study evolutionary diversity and gene family evolution.