Accurate genome-wide detection of somatic mutations with low variant allele frequency (VAF, <1%) has proven difficult, for which generalized, scalable methods are lacking. Herein, we describe a new computational method, called RePlow that we developed to detect low-VAF somatic mutations based on simple, library-level replicates for next-generation sequencing on any platform. Through joint analy...

BACKGROUND Leptospirosis is the most widespread zoonotic disease. It is caused by infection with pathogenic Leptospira species, of which over 300 serovars have been described. The accurate identification of the causative Leptospira spp. is required to ascertain the pathogenic status of the local isolates. OBJECTIVES This study aimed to obtain the complete genome sequence of a virulent Leptospir...

Objective. Systemic lupus erythematosus (SLE) isa chronic and heterogeneous autoimmune disease. Both twin and sibling studies indicate a strong genetic contribution to lupus, but in the majority of cases the pathogenic variant remains to be identified. The genetic contribution to disease is likely to be greatest in cases with early onset and severe phenotypes. Whole-exome sequencing now offers ...

Hereditary spastic paraplegia (HSP) is a group of neurodegenerative diseases with genetic and clinical heterogeneity characterized by spasticity weakness the lower limbs. It includes four inheritance forms: autosomal dominant (AD), recessive (AR), X-linked inheritance, mitochondrial inheritance. To date, more than 82 gene loci have been found to cause HSP, SPG15 ( ZFYVE26 ) one most common here...

Diagnostic tests based on next-generation sequencing (NGS), including gene-panel, exome, and wholegenome sequencing, are routinely performed worldwide. Although the technical validity of NGS-based tests continues to improve rapidly, the community is working to demonstrate the clinical validity and utility of these methods, which largely depend on our ability to interpret all sequence variants i...

AIM The corneal dystrophies represent a group of clinically and genetically heterogeneous, inherited diseases, often resulting in bilateral opacification of the cornea, and may require penetrating keratoplasty. Mutations in the transforming growth factor beta-induced (TGFBI) gene segregate with a wide range of phenotypically heterogeneous corneal dystrophies. Many of the other dystrophies remai...

BACKGROUND The reported penetrance of germline CDH1 mutations is high in families with hereditary diffuse gastric cancer (HDGC). Men and women have a 70% and 56%, respectively, cumulative risk of developing diffuse gastric cancer by age 80. Women additionally have a 42% cumulative risk of developing breast cancer. Due to the high penetrance of these mutations, prophylactic total gastrectomy is ...

OBJECTIVE To determine the genetic etiology of a young woman presenting an early-onset, progressive neurodegenerative disorder with evidence of decreased mitochondrial complex I and IV activities in skeletal muscle suggestive of a mitochondrial disorder. METHODS A case report including diagnostic workup, whole-exome sequencing of the affected patient, filtering, and prioritization of candidat...

The development of high-throughput technologies such as next-generation sequencing (NGS) has allowed for thousands of DNA loci to be interrogated simultaneously in a fast and economical method for the detection of clinically deleterious variants. Whenever a clinical diagnosis is known, a targeted NGS approach involving the use of disease-specific gene panels can be employed. This approach is of...

This case report describes an individual with brain calcifications, cognitive decline, motor dysfunction, and hypocalcaemia. Exome sequencing revealed a previously reported variant in the CASR gene and a variant of uncertain significance in PDGFRB. The clinical phenotype is likely explained by the CASR variant, but we discuss how the PDGFRB variant could also participate in the phenotype.