Genomic variations and chromosomal abnormalities

This study identifies technical challenges in detecting somatic recombination of repeat elements using short and long read datasets and highlights PCR-induced artifacts.

The paper identifies breakage-replication/fusion as a mechanism causing DNA duplications and insertions, unifying explanations for complex rearrangements and enabling rapid DNA amplification.

This paper introduces SMM-SV-seq, a method to detect rare somatic structural-variant breakpoints in bulk DNA with high precision and recall, validated using human and Drosophila DNA mixtures and clinical treatments.

The paper constructs TRCompDB, a database of 4.4 million tandem repeat loci across 832 human genomes, revealing mutation rates and dynamics influenced by recombination and duplication context.

This paper introduces colorSV, a method for calling long-range somatic structural variants using co-assembly graphs, achieving high precision and sensitivity in translocation detection.

The paper analyzes optical mapping data from Black and white genomes to reveal structural differences in 22q11.2 low copy repeats (LCR22s) and their potential role in the lower prevalence of 22q11.2DS in Black individuals.

This study examines how dup15q affects gene expression and chromatin accessibility in specific brain cell types, finding cell-type-specific effects and distinct regulatory mechanisms in ASD and dup15q.

The paper investigates the impact of rare high-effect genetic variants on brain morphology and related behavioral traits in adolescents using the ABCD cohort.

This study identifies copy number variants (CNVs) associated with child psychopathology and cognitive function using data from the ABCD study.

AmpliconSuite identifies focal amplifications in cancer genomes, showing ecDNA has higher copy numbers and stronger oncogene enrichment compared to other amplification types.

The paper investigates how different genome references affect inversion detection, showing that T2T-CHM13 and long-read sequencing improve resolution of challenging inversions.

The paper identifies de novo retroelements in birth defects and childhood cancers using whole-genome sequencing data and an improved computational tool.

This study identifies de novo structural variants in a large cohort of rare disease patients, highlighting their prevalence and potential pathogenicity.

msCNVS enables efficient CNV profiling of rare clinical samples through barcoded single-cell library construction without preamplification.

This paper shows that using a complete reference genome improves the accuracy and reduces false positives in detecting structural variants in cancer genomes.

The paper investigates the mechanisms behind the high incidence of 22q11.2 deletion syndrome by analyzing recombination events and paralogous structures in LCR22 regions.

The paper characterizes a VNTR in CACNA1C associated with schizophrenia, showing linkage to risk variants and reduced gene expression.

SVarp discovers haplotype-resolved structural variants using a pangenome reference and long reads, achieving high recall in simulated and real data.

This study shows that Tbx1 haploinsufficiency in mice causes brain metabolic and behavioral issues, which are partially reversed by vitamin B12 treatment.

The paper identifies a novel neurodevelopmental disorder caused by de novo deletion of the lncRNA CHASERR, showing its role in regulating CHD2 expression and causing developmental and epileptic encephalopathy.

The paper characterizes intrachromosomal repeats in three human genome assemblies, finding more repeats in the T2T-CHM13 assembly and identifying gene categories enriched for repeat-associated genomic disorders.

This study evaluates Optical Genome Mapping (OGM) for detecting structural variants in myeloid neoplasms, showing high concordance and identifying additional clinically relevant variants compared to standard of care methods.

KAGE2 improves structural variant genotyping by using pangenomes, offering higher accuracy and speed compared to existing methods.

CytoCellDB is a database that expands the number of cancer cell lines with ecDNA annotations, enabling analysis of ecDNA in relation to molecular data and drug responses.

This study evaluates HiFi Revio long-read sequencing for detecting chromosomal rearrangements in rare diseases, showing high accuracy for breakpoint junctions and derivative chromosome structures.

This study maps individual brain deviation scores in individuals with pathogenic CNVs using normative modeling and shows correlations between negative deviations and cognitive function.

The paper uses random forest classifiers trained on simulated data to accurately genotype structural variants in the alpha globin region, outperforming existing software in ancestry-specific allele frequency estimation.

This study identifies lobule VI-specific structural and functional cerebellar abnormalities in 16p11.2 microduplication mice, linking them to learning impairments and neuropsychiatric disorder symptoms.

KmerSV visualizes and annotates structural variants using k-mers and the Human Pangenome reference.

The paper compares germline and somatic structural variants in cancer, identifying differences in their generating processes and selection, and develops a classifier to distinguish them in tumor samples without matched normals.