Genomic variations and chromosomal abnormalities

CNVpytor: a tool for CNV/CNA detection and analysis from read depth and allele imbalance in whole genome sequencing

CNVpytor is a Python-based tool for detecting and analyzing CNVs/CNAs from whole genome sequencing data, offering improved speed, functionality, and visualization compared to CNVnator.

Genotyping of structural variation using PacBio high-fidelity sequencing

This study evaluates SV detection using PacBio HiFi sequencing in wheat genomes, finding that aligners and callers significantly impact accuracy and that low-coverage HiFi sequencing can generate high-quality SV genotypes.

Network-based analysis of allele frequency distribution among multiple populations identifies adaptive genomic structural variants

The paper identifies adaptive genomic structural variants across 26 populations using a network-based method and finds 577 variants with high population distribution, some overlapping with coding sequences or GWAS traits.

Enhancing breakpoint resolution with deep segmentation model: a general refinement method for read-depth based structural variant callers

RDBKE improves breakpoint resolution of read-depth SV callers using a deep segmentation model, increasing the number of SVs with more precise breakpoints on simulation and real data.

HyINDEL - A Hybrid approach for Detection of Insertions and Deletions

HyINDEL improves INDEL detection by integrating clustering, split-mapping, and assembly-based methods, showing better recall and F-score on simulated and real data.

RCytoGPS: An R Package for Reading and Visualizing Cytogenetics Data

RCytoGPS converts JSON karyotype data into R objects for analysis and visualization, streamlining computational cytogenetic pathology.

An ensemble deep learning framework to refine large deletions in linked-reads

AquilaDeepFilter improves the precision of large deletion SV detection from linked-reads by using a deep learning ensemble, while maintaining high recall and outperforming existing methods.

MARS: a tool for haplotype-resolved population-based structural variation detection

MARS detects haplotype-resolved structural variants from linked-read assemblies using Mendelian inheritance and HiFi reads, achieving 73%-87% validation rates for indels.

Viola: a structural variant signature extractor with user-defined classifications

Viola extracts biologically meaningful structural variant signatures from cancer data and provides tools for custom classification and annotation.

Reciprocal differentiation via GABAergic components and ASD-related phenotypes in hES with 1q21.1 CNV

This study generates isogenic hES cell lines with reciprocal 1q21.1 CNVs and shows opposite differentiation outcomes and shared hyperexcitability features.

High resolution copy number inference in cancer using short-molecule nanopore sequencing

This paper demonstrates that sequencing short DNA molecules with nanopore sequencing improves copy number inference in cancer, offering higher sensitivity and accuracy compared to traditional methods.

Pharmacological rescue of the brain cortex phenotype in Tbx1 mouse mutants: significance for 22q11.2 deletion syndrome

This study identifies two drugs that rescue the brain cortex phenotype in Tbx1 mutant mice, suggesting potential therapeutic strategies for 22q11.2 deletion syndrome.

Genomic and transcriptomic analyses reveal a tandem amplification unit of 11 genes and mutations of mismatch repair genes in methotrexate-resistant HT-29 cells

Cortical Organoids Model Early Brain Development Disrupted by 16p11.2 Copy Number Variants in Autism

This study uses cortical organoids derived from patients with 16p11.2 CNV to show altered neurodevelopmental processes, including changes in organoid size, neuronal maturation, and migration.

Characterizing nucleotide variation and expansion dynamics in human-specific variable number tandem repeats

The paper characterizes human-specific VNTRs by analyzing their nucleotide composition and expansion dynamics across genomes and populations.

Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease

The paper identifies 21 candidate haploinsufficient genes associated with congenital heart disease through integrative analysis of CNVs and DNMs in CHD cases and controls.

Alterations in neuronal physiology, development, and function associated with a common duplication of chromosome 15 involving CHRNA7

This study uses iPSC models to show that a 15q13.3 duplication causes distinct neurodevelopmental and functional anomalies in an affected individual but not their unaffected mother, while both share increased cholinergic activity.

Caregiver perspectives on a diagnosis of 3q29 deletion

This study explores caregiver experiences and concerns following a diagnosis of 3q29 deletion syndrome, highlighting gaps in communication about future psychosis risk.

Mako: a graph-based pattern growth approach to detect complex structural variants

Mako detects complex structural variants using a graph-based pattern growth approach, achieving 70% validation rate on real data and identifying 15 CSV types including two novel ones.

BMI-CNV: A Bayesian framework for multiple genotyping platforms detection of copy number variation

BMI-CNV improves CNV detection by integrating WES and microarray data across samples, showing better accuracy and identifying lung cancer risk regions.

Convergent and distributed effects of the schizophrenia-associated 3q29 deletion on the human neural transcriptome

This study investigates the molecular effects of the 3q29 deletion on the human neural transcriptome, identifying convergent and distributed impacts across gene clusters and pathways related to psychiatric disorders.

Using induced pluripotent stem cells to investigate human neuronal phenotypes in 1q21.1 deletion and duplication syndrome.

This study investigates the effects of 1q21.1 deletion and duplication on neuronal development using induced pluripotent stem cells and shows reciprocal phenotypes and potential therapeutic targets.

Sex-specific recombination predicts parent of origin for recurrent genomic disorders

The paper shows that sex-specific differences in meiotic recombination rates are associated with parental origin biases in recurrent genomic disorders.

Deep Learning Approach to Genomic Breakage Study from Primary Sequence

This study introduces FusionAI, a deep learning model that predicts gene fusion breakpoints from DNA sequences, aiding in the identification of genomic breakage mechanisms.

Characterization of Structural Variation in Tibetans Reveals New Evidence of High-altitude Adaptation and Introgression

This study identifies structural variations in Tibetans and Han populations, revealing adaptive SVs and introgression linked to high-altitude adaptation.

Samplot: A Platform for Structural Variant Visual Validation and Automated Filtering

Samplot creates visualizations for structural variant validation and includes a machine learning tool to reduce false positives across multiple sequencing technologies.

Genome-wide Copy Number Variations in a Large Cohort of Bantu African Children

This study identifies over 400,000 CNVs in 3400 Bantu African children, highlighting common CNVs overlapping disease-associated genes and providing a large dataset for African ancestry CNV research.

Long read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits

The paper uses long-read sequencing on 3,622 Icelanders to identify structural variants and their associations with diseases and traits.

Determination of complete chromosomal haplotypes by bulk DNA sequencing

This paper presents a computational method to determine complete chromosomal haplotypes using bulk long-range sequencing and Hi-C data, achieving high precision and completeness in diploid human genomes.

Virus-derived variation in diverse human genomes

The paper develops computational tools to study virus-derived structural variants in human genomes, identifying new somatic and heritable variants from retroviruses and uncovering their potential impact on gene expression and genetic diversity.