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Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project
BackgroundA major obstacle faced by families with rare diseases is obtaining a genetic diagnosis. The average "diagnostic odyssey" lasts over five...
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A recurrent synonymous L1CAM variant in a fetus with hydrocephalus
We report the case of a hydrocephalic fetus in which clinical exome sequencing revealed a recurrent synonymous variant of unknown significance,...
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Variant calling and benchmarking in an era of complete human genome sequences
Genetic variant calling from DNA sequencing has enabled understanding of germline variation in hundreds of thousands of humans. Sequencing...
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Detection of a major Lynch Syndrome-causing MLH1 founder variant in a large-scale genotyped cohort
Some 50% of Finnish Lynch Syndrome (LS) cases are caused by a founder variant in MLH1 , in which the entire exon 16 has been lost due to an...
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An optimized GATK4 pipeline for Plasmodium falciparum whole genome sequencing variant calling and analysis
BackgroundAccurate variant calls from whole genome sequencing (WGS) of Plasmodium falciparum infections are crucial in malaria population genomics....
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Beyond gene-disease validity: capturing structured data on inheritance, allelic requirement, disease-relevant variant classes, and disease mechanism for inherited cardiac conditions
BackgroundAs the availability of genomic testing grows, variant interpretation will increasingly be performed by genomic generalists, rather than...
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Identification of a missense variant of MND1 in meiotic arrest and non-obstructive azoospermia
Meiotic arrest is a common pathologic phenotype of non-obstructive azoospermia (NOA), yet its genetic causes require further investigation. Meiotic...
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MmisAT and MmisP: an efficient and accurate suite of variant analysis toolkit for primary mitochondrial diseases
Recent advances in next-generation sequencing (NGS) technology have greatly accelerated the need for efficient annotation to accurately interpret...
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Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies
Meta-analysis of whole genome sequencing/whole exome sequencing (WGS/WES) studies provides an attractive solution to the problem of collecting large...
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A common flanking variant is associated with enhanced stability of the FGF14-SCA27B repeat locus
The factors driving or preventing pathological expansion of tandem repeats remain largely unknown. Here, we assessed the FGF14 (GAA)·(TTC) repeat...
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Waardenburg syndrome type 2 with a de novo variant of the SOX10 gene: a case report
BackgroundWaardenburg syndrome type 2 (WS2) has been reported to be a rare hereditary disorder, which is distinguished by vivid blue eyes, varying...
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Neurofibromatosis-Noonan syndrome and growth deficiency in an Iranian girl due to a pathogenic variant in NF1 gene
BackgroundMutations in NF1 gene could cause allelic disorders with clinical spectrum of Neurofibromatosis type 1 to Noonan syndrome. Here, a...
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Somatic and Germline Variant Calling from Next-Generation Sequencing Data
Re-sequencing of the human genome by next-generation sequencing (NGS) has been widely applied to discover pathogenic genetic variants and/or...
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A Heterozygous Phospholamban Variant (p.R14del) Leads to Left Ventricular Involvement and Heart Failure Phenotypes in Arrhythmogenic Right Ventricular Cardiomyopathy
This study aimed to determine the prevalence and clinical features of Arrhythmogenic Right Ventricular Cardiomyopathy (ARVC) caused by pathogenic...
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Effective variant filtering and expected candidate variant yield in studies of rare human disease
In studies of families with rare disease, it is common to screen for de novo mutations, as well as recessive or dominant variants that explain the...
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GeneTerpret: a customizable multilayer approach to genomic variant prioritization and interpretation
BackgroundVariant interpretation is the main bottleneck in medical genomic sequencing efforts. This usually involves genome analysts manually...
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A novel nonsense variant in the CENPP gene segregates in a Swiss family with autosomal dominant low-frequency sensorineural hearing loss
Low-frequency sensorineural hearing loss (SNHL) is a rare hearing impairment affecting frequencies below 1000 Hz, previously associated with DIAPH1,...
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AIVariant: a deep learning-based somatic variant detector for highly contaminated tumor samples
The detection of somatic DNA variants in tumor samples with low tumor purity or sequencing depth remains a daunting challenge despite numerous...
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Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank
Phasing involves distinguishing the two parentally inherited copies of each chromosome into haplotypes. Here, we introduce SHAPEIT5, a new phasing...
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Epilepsia Partialis Continua a Clinical Feature of a Missense Variant in the ADCK3 Gene and Poor Response to Therapy
IntroductionCoenzyme Q10 deficiency can be due to mutations in Coenzyme Q10-biosynthesis genes (primary) or genes unrelated to biosynthesis...
