Hum Mutat [journal]
- Acute Intermittent Porphyria: Predicted Pathogenicity of HMBS Variants Indicates Extremely Low Penetrance of the Autosomal Dominant Disease. [JOURNAL ARTICLE]
- Hum Mutat 2016 Aug 19.
Acute Intermittent Porphyria results from hydroxymethylbilane synthase (HMBS) mutations that markedly decrease HMBS enzymatic activity. This dominant disease is diagnosed when heterozygotes have life-threatening acute attacks, while most heterozygotes remain asymptomatic and undiagnosed. Although > 400 HMBS mutations have been reported, the prevalence of pathogenic HMBS mutations in genomic/exomic databases, and the actual disease penetrance are unknown. Thus, we interrogated genomic/exomic databases, identified non-synonymous variants (NSVs) and consensus splice-site variants (CSSVs) in various demographic/racial groups, and determined the NSV's pathogenicity by prediction algorithms and in vitro expression assays. Caucasians had the most: 58 NSVs and two CSSVs among ∼ 92,000 alleles, a 0.00575 combined allele frequency. In silico algorithms predicted 14/58 NSVs as "likely-pathogenic". In vitro expression identified 10/58 NSVs as likely-pathogenic (seven predicted in silico), which together with two CSSVs had a combined allele frequency of 0.00056. Notably, six presumably pathogenic mutations/NSVs in the Human Gene Mutation Database were benign. Compared to the recent prevalence estimate of symptomatic European heterozygotes (∼ 0.000005), the prevalence of likely-pathogenic HMBS mutations among Caucasians was > 100 times more frequent. Thus, the estimated penetrance of acute attacks was ∼ 1% of heterozygotes with likely-pathogenic mutations, highlighting the importance of predisposing/protective genes and environmental modifiers that precipitate/prevent the attacks. This article is protected by copyright. All rights reserved.
- Mini-Exome Coupled to Read-Depth Based Copy Number Variation Analysis in Patients with Inherited Ataxias. [JOURNAL ARTICLE]
- Hum Mutat 2016 Aug 16.
Next generation sequencing (NGS) has an established diagnostic value for inherited ataxia. However, the need of a rigorous process of analysis and validation remains challenging. Moreover, copy number variations (CNV) or dynamic expansions of repeated sequence are classically considered not adequately detected by exome sequencing technique. We applied a strategy of mini-exome coupled to read-depth based CNV analysis to a series of 33 patients with probable inherited ataxia and onset <50 years. The mini-exome consisted of the capture of 4813 genes having associated clinical phenotypes. Pathogenic variants were found in 42% and variants of uncertain significance in 24% of the patients. These results are comparable to those from whole exome sequencing and better than previous targeted NGS studies. CNV and dynamic expansions of repeated CAG sequence were identified in three patients. We identified both atypical presentation of known ataxia genes (ATM, NPC1) and mutations in genes very rarely associated with ataxia (ERCC4, HSD17B4). We show that mini-exome bioinformatics data analysis allows the identification of CNV and dynamic expansions of repeated sequence. Our study confirms the diagnostic value of the proposed genetic analysis strategy. We also provide an algorithm for the multidisciplinary process of analysis, interpretation, and validation of NGS data. This article is protected by copyright. All rights reserved.
- Non-coding RNA: Current Deep Sequencing Data Analysis Approaches and Challenges. [REVIEW, JOURNAL ARTICLE]
- Hum Mutat 2016 Aug 12.
One of the most significant biological discoveries of the past decade is represented by the reality that the vast majority of the transcribed genomic output is comprised of diverse classes of non-coding RNAs (ncRNAs) that may play key roles and/or be affected by many biochemical cellular processes (i.e. RNA editing), with implications in human health and disease. With 90% of the human genome being transcribed and novel classes of ncRNA emerging (tRNA-derived small RNAs and circular RNAs among others), the great majority of the human transcriptome suggests that many important ncRNA functions/processes are yet to be discovered. An approach to filling such vast void of knowledge has been recently provided by the increasing application of next-generation sequencing (NGS), offering the unprecedented opportunity to obtain a more accurate profiling with higher resolution, increased throughput, sequencing depth, and low experimental complexity, concurrently posing an increasing challenge in terms of efficiency, accuracy and usability of data analysis software. This review provides an overview of ncRNAs, NGS technology and the most recent/popular computational approaches and the challenges they attempt to solve, which are essential to a more sensitive and comprehensive ncRNA annotation capable of furthering our understanding of this still vastly uncharted genomic territory. This article is protected by copyright. All rights reserved.
- Silent or Not Silent? Consequences of the Human mt-cyb Polymorphism. [Journal Article]
- Hum Mutat 2016 Sep; 37(9):833.
- Base-biased Evolution of Disease-associated Mutations in the Human Genome. [JOURNAL ARTICLE]
- Hum Mutat 2016 Aug 10.
Understanding the evolution of disease-associated mutations is fundamental to analyze pathogenetics of diseases. Mutation, recombination (by GC biased gene conversion, gBGC) and selection have been known to shape the evolution of disease-associated mutations, but how these evolutionary forces work together is still an open question. In this study we analyzed several human large-scale datasets (1000 Genomes, ESP6500, ExAC and ClinVar), and found that base-biased mutagenesis generates more GC→AT than AT→GC mutations, while gBGC promotes the fixation of AT→GC mutations to balance the impact of base-biased mutation on genome. Due to this effect of gBGC, purifying selection removes more deleterious AT→ GC mutations than GC→AT from population, but many high-frequency (fixed and nearly fixed) deleterious AT→ GC mutations are remained possibly due to high genetic load. As a special subset, disease-associated mutations follow this evolutionary rule, in which disease-associated GC→AT mutations are more enriched in rare mutations compared to AT→GC, while disease-associated AT→GC are more enriched in mutations with high frequency. Thus we presented a base-biased evolutionary framework that explains the base-biased generation and accumulation of disease-associated mutations in human populations. This article is protected by copyright. All rights reserved.
- Molecular Chaperones in the Pathogenesis of Amyotrophic Lateral Sclerosis: the role of HSPB1. [JOURNAL ARTICLE]
- Hum Mutat 2016 Aug 5.
Genetic discoveries in Amyotrophic Lateral Sclerosis (ALS) have a significant impact on deciphering molecular mechanisms of motor neuron degeneration but, despite recent advances, the aetiology of most sporadic cases remains elusive. Several cellular mechanisms contribute to the motor neuron degeneration in ALS, including RNA metabolism, cellular interactions between neurons and non-neuronal cells and seeding of misfolded protein with prion-like propagation. In this scenario, the importance of protein turnover and degradation in motor neuron homeostasis gained increased recognition. In this study, we evaluated the role of the candidate gene HSPB1, a molecular chaperone involved in several proteome-maintenance functions. In a cohort of 247 unrelated Italian ALS patients, we identified two variants (c.570G>C, p.Gln190His and c.610dupG, p.Ala204Glyfs*6). Functional characterization of the p.Ala204Glyfs*6 demonstrated that the mutant protein alters HSPB1 dynamic equilibrium, sequestering the wild-type protein in a stable dimer and resulting in a loss of chaperone-like activity. Our results underline the relevance of identifying rare but pathogenic variations in sporadic neurodegenerative diseases, suggesting a possible correlation between specific pathomechanisms linked to HSPB1 mutations and the associated neurological phenotype. Our study provides additional lines of evidence to support the involvement of HSPB1 in the pathogenesis of sporadic ALS. This article is protected by copyright. All rights reserved.
- Loss of Major DNase I Hypersensitive Sites in Duplicated β-globin Gene Cluster Incompletely Silences HBB Gene Expression. [JOURNAL ARTICLE]
- Hum Mutat 2016 Aug 5.
We report an infant with sickle cell disease phenotype by biochemical analysis whose β-globin gene (HBB) sequencing showed sickle cell mutation (HBB(S) ) heterozygosity. The proband has a unique head-to-tail duplication of the β-globin gene cluster having wild-type (HBB(A) ) and HBB(S) alleles inherited from her father; constituting her HBB(S) /HBB(S) -HBB(A) genotype. Further analyses revealed that proband's duplicated β-globin gene cluster (∼650 kb) encompassing HBB(A) does not include the immediate upstream locus control region (LCR) or 3' DNase I hypersensitivity (HS) element. The LCR interacts with β-globin gene cluster involving long range DNA interactions mediated by various transcription factors to drive the regulation of globin genes expression. However, a low level of HBB(A) transcript was clearly detected by digital PCR. In this patient, the observed transcription from the duplicated, distally displaced HBB(A) cluster demonstrates that the loss of LCR and flanking 3'HS sites do not lead to complete silencing of HBB transcription.
- Brief ReportNovel Genetic, Clinical and Pathomechanistic Insights into TFG-Associated Hereditary Spastic Paraplegia. [JOURNAL ARTICLE]
- Hum Mutat 2016 Aug 5.
Hereditary spastic paraplegias (HSPs) are genetically and clinically heterogeneous axonopathies primarily affecting upper motor neurons and, in complex forms, additional neurons. Here, we report two families with distinct recessive mutations in TFG, previously suggested to cause HSP based on findings in a single small family with complex HSP. The first carried a homozygous c.317G>A (p.R106H) variant and presented with pure HSP. The second carried the same homozygous c.316C>T (p.R106C) variant previously reported and displayed a similarly complex phenotype including optic atrophy. Haplotyping and bisulfate sequencing revealed evidence for a c.316C>T founder allele, as well as for a c.316_317 mutation hotspot. Expression of mutant TFG proteins in cultured neurons revealed mitochondrial fragmentation, the extent of which correlated with clinical severity. Our findings confirm the causal nature of bi-allelic TFG mutations for HSP, broaden the clinical and mutational spectra, and suggest mitochondrial impairment to represent a pathomechanistic link to other neurodegenerative conditions. This article is protected by copyright. All rights reserved.
- Clinical Interpretation of Variants from Next-Generation Sequencing: The 2016 Scientific Meeting of the Human Genome Variation Society. [JOURNAL ARTICLE]
- Hum Mutat 2016 Aug 5.
The 2016 scientific meeting of the Human Genome Variation Society (HGVS; http://www.hgvs.org) was held on the 20th of May in Barcelona, Spain, with the theme of "Clinical Interpretation of Variants from Next-Generation Sequencing."