Sarah B. Kingan

Whole-genome variant detection in long-read sequencing data from ultra-low input patient samples

This study evaluates ULI-HiFi and dMDA for long-read sequencing of low-input samples, finding ULI-HiFi achieves higher variant detection accuracy and reveals disease-relevant genetic changes in a FAP patient.

Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair

The paper describes a comprehensive genomic dataset from a tumor-normal pair with broad consent, generated using multiple sequencing technologies for benchmarking somatic variant detection.

CCG interruptions are unstable and hypermethylated in DM1 patients

This study shows CCG interruptions in DM1 are unstable and hypermethylated, contributing to CTG repeat stabilization.

Closing the gap: Solving complex medically relevant genes at scale

The paper introduces a targeted sequencing framework, TADGP, that accurately calls variants in complex medically relevant genes at lower cost than HiFi-WGS, enabling scalable analysis of dark genomic regions.

Design and performance of a long-read sequencing panel for pharmacogenomics

The paper presents a long-read sequencing panel for pharmacogenomics, achieving high accuracy and phasing for SNVs and clinical star(*)-alleles.

Towards complete and error-free genome assemblies of all vertebrate species

The paper summarizes methods and lessons from assembling 16 vertebrate genomes, highlights the importance of long-read sequencing, and introduces the Vertebrate Genomes Project to generate complete reference genomes for all vertebrate species.

Extended haplotype phasing of de novo genome assemblies with FALCON-Phase

FALCON-Phase uses long-read sequencing and Hi-C data to create phased diploid genome assemblies, achieving high accuracy in non-human species but lower accuracy in humans.

A phased, diploid assembly of the Cascade hop (Humulus lupulus) genome reveals patterns of selection and haplotype variation

The paper presents a phased diploid assembly of the Cascade hop genome, revealing patterns of selection and haplotype variation, and identifies a homolog of CBDAS.

Sequence and annotation of 42 cannabis genomes reveals extensive copy number variation in cannabinoid synthesis and pathogen resistance genes

Long-read assemblies of an inbred cannabis trio plus whole-genome sequencing of 40 cultivars link cannabinoid synthase gene deletions to chemotype and associate CsTLP1 loss with powdery mildew susceptibility.

Genomic Analysis of Powdery Mildew Resistance in a Hop (Humulus lupulus L.) Bi-parental Population Segregating for R6-locus

The paper re-evaluates powdery mildew resistance in hop using QTL analysis and RNAseq, identifying genomic regions and gene expression patterns associated with resistance to races v4/v6.

A High-Quality Genome Assembly from a Single, Field collected Spotted Lanternfly (Lycorma delicatula) using the PacBio Sequel II System

The paper presents a high-quality genome assembly of a field-collected Spotted Lanternfly using PacBio long-read sequencing, achieving high contiguity and completeness.

Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation

The paper presents haplotype-resolved cattle genomes to identify structural variants and adaptation traits, finding expanded immune-related gene families and a fatty acid desaturase copy under positive selection in indicine cattle.

A High-Quality De Novo Genome Assembly from a Single Mosquito using PacBio Sequencing

This paper presents a high-quality de novo genome assembly of a single Anopheles coluzzii mosquito using a modified PacBio protocol, achieving high contiguity and completeness with low DNA input.

Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control

The paper presents an improved Aedes aegypti genome assembly, AaegL5, which enhances biological understanding and vector control efforts by resolving key genomic features and identifying new targets for intervention.

Complete assembly of parental haplotypes with trio binning

This paper introduces trio binning, a method for assembling haplotypes from heterozygous genomes using parental short reads, achieving high accuracy in diploid reconstruction.

A high-quality, long-read de novo genome assembly to aid conservation of Hawaii’s last remaining crow species

The paper presents a high-quality long-read genome assembly for the Alala, a critically endangered Hawaiian crow, to support conservation efforts through genomic tools and comparative studies.

The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum

The paper presents the first near-complete assembly of the hexaploid bread wheat genome using a combination of short and long-read sequencing technologies.

De Novo PacBio long-read and phased avian genome assemblies correct and add to genes important in neuroscience research

The paper uses PacBio long-read sequencing to generate high-quality, phased genome assemblies for zebra finch and hummingbird, correcting gene structure errors in neuroscience-relevant genes.