VCF.Filter: interactive prioritization of disease-linked genetic variants from sequencing data.

Nucleic Acids Res. 2017 May 17;:

Authors: Müller H, Jimenez-Heredia R, Krolo A, Hirschmugl T, Dmytrus J, Boztug K, Bock C

Abstract
Next generation sequencing is widely used to link genetic variants to diseases, and it has massively accelerated the diagnosis and characterization of rare genetic diseases. After initial bioinformatic data processing, the interactive analysis of genome, exome, and panel sequencing data typically starts from lists of genetic variants in VCF format. Medical geneticists filter and annotate these lists to identify variants that may be relevant for the disease under investigation, or to select variants that are reported in a clinical diagnostics setting. We developed VCF.Filter to facilitate the search for disease-linked variants, providing a standalone Java program with a user-friendly interface for interactive variant filtering and annotation. VCF.Filter allows the user to define a broad range of filtering criteria through a graphical interface. Common workflows such as trio analysis and cohort-based filtering are pre-configured, and more complex analyses can be performed using VCF.Filter's support for custom annotations and filtering criteria. All filtering is documented in the results file, thus providing traceability of the interactive variant prioritization. VCF.Filter is an open source tool that is freely and openly available at http://vcffilter.rarediseases.at.

PMID: 28520890 [PubMed - as supplied by publisher]

Using high-resolution variant frequencies to empower clinical genome interpretation.

Genet Med. 2017 May 18;:

Authors: Whiffin N, Minikel E, Walsh R, O'Donnell-Luria AH, Karczewski K, Ing AY, Barton PJR, Funke B, Cook SA, MacArthur D, Ware JS

Abstract
PurposeWhole-exome and whole-genome sequencing have transformed the discovery of genetic variants that cause human Mendelian disease, but discriminating pathogenic from benign variants remains a daunting challenge. Rarity is recognized as a necessary, although not sufficient, criterion for pathogenicity, but frequency cutoffs used in Mendelian analysis are often arbitrary and overly lenient. Recent very large reference datasets, such as the Exome Aggregation Consortium (ExAC), provide an unprecedented opportunity to obtain robust frequency estimates even for very rare variants.MethodsWe present a statistical framework for the frequency-based filtering of candidate disease-causing variants, accounting for disease prevalence, genetic and allelic heterogeneity, inheritance mode, penetrance, and sampling variance in reference datasets.ResultsUsing the example of cardiomyopathy, we show that our approach reduces by two-thirds the number of candidate variants under consideration in the average exome, without removing true pathogenic variants (false-positive rate<0.001).ConclusionWe outline a statistically robust framework for assessing whether a variant is "too common" to be causative for a Mendelian disorder of interest. We present precomputed allele frequency cutoffs for all variants in the ExAC dataset.GENETICS in MEDICINE advance online publication, 18 May 2017; doi:10.1038/gim.2017.26.

PMID: 28518168 [PubMed - as supplied by publisher]

DNA Sequence Analysis in Clinical Medicine, Proceeding Cautiously.

Front Mol Biosci. 2017;4:24

Authors: Smith M

Abstract
Delineation of underlying genomic and genetic factors in a specific disease may be valuable in establishing a definitive diagnosis and may guide patient management and counseling. In addition, genetic information may be useful in identification of at risk family members. Gene mapping and initial genome sequencing data enabled the development of microarrays to analyze genomic variants. The goal of this review is to consider different generations of sequencing techniques and their application to exome sequencing and whole genome sequencing and their clinical applications. In recent decades, exome sequencing has primarily been used in patient studies. Discussed in some detail, are important measures that have been developed to standardize variant calling and to assess pathogenicity of variants. Examples of cases where exome sequencing has facilitated diagnosis and led to improved medical management are presented. Whole genome sequencing and its clinical relevance are presented particularly in the context of analysis of nucleotide and structural genomic variants in large population studies and in certain patient cohorts. Applications involving analysis of cell free DNA in maternal blood for prenatal diagnosis of specific autosomal trisomies are reviewed. Applications of DNA sequencing to diagnosis and therapeutics of cancer are presented. Also discussed are important recent diagnostic applications of DNA sequencing in cancer, including analysis of tumor derived cell free DNA and exosomes that are present in body fluids. Insights gained into underlying pathogenetic mechanisms of certain complex common diseases, including schizophrenia, macular degeneration, neurodegenerative disease are presented. The relevance of different types of variants, rare, uncommon, and common to disease pathogenesis, and the continuum of causality, are addressed. Pharmogenetic variants detected by DNA sequence analysis are gaining in importance and are particularly relevant to personalized and precision medicine.

PMID: 28516087 [PubMed - in process]

Carrier frequency of Wilson's disease in the Korean population: a DNA-based approach.

J Hum Genet. 2017 May 18;:

Authors: Jang JH, Lee T, Bang S, Kim YE, Cho EH

Abstract
Wilson's disease (WD) is an autosomal recessive disorder caused by ATP7B gene mutation. The frequency of WD is about 1 in 30 000 worldwide. In the present study, we screened 14 835 dried blood spots (DBSs) from asymptomatic Korean neonates and retrospectively reviewed massively parallel sequencing of 1090 control individuals to estimate carrier frequency. TaqMan real-time PCR assays were conducted to detect six mutations that account for 58.3% of mutations in Korean WD patients: c.2333G>T (p.Arg778Leu), c.2621C>T (p.Ala874Val), c.3086C>T (p.Thr1029Ile), c.3247C>T (p.Leu1083Phe), c.3556G>A (p.Gly1186Ser) and c.3809A>G (p.Asn1270Ser). We also retrospectively reviewed data from 1090 individuals with various indications other than WD for whom whole-exome or panel sequencing data were available. Mutant allele frequency based on the six most common mutations was 0.0067 among the total of 14 835 DBSs screened. Given that these six mutations account for 58.3% of mutations in Korean WD patients, the corrected mutant allele frequency is 0.0115 (95% confidence interval (CI): 0.0103-0.0128). Corresponding incidence (q(2)) and carrier frequency (2pq) were estimated to be 1:7561 and 1:44, respectively. In retrospective data analysis of 1090 control individuals, allele frequency of pathogenic or likely pathogenic variants was 0.0096 (95% CI: 0.0063-0.0146). Corresponding carrier frequency was estimated to be 1:53. Estimated allele and carrier frequencies based on DNA screening were relatively higher than those reported previously based on clinical ascertainment.Journal of Human Genetics advance online publication, 18 May 2017; doi:10.1038/jhg.2017.49.

PMID: 28515472 [PubMed - as supplied by publisher]

Identification of somatic mutations using whole-exome sequencing in Korean patients with acute myeloid leukemia.

BMC Med Genet. 2017 Mar 01;18(1):23

Authors: Heo SG, Koh Y, Kim JK, Jung J, Kim HL, Yoon SS, Park JW

Abstract
BACKGROUND: Acute myeloid leukemia (AML) is a biologically and clinically heterogeneous cancer of the bone marrow that is characterized by the rapid growth of abnormal myeloid cells.
METHODS: We performed a mutational analysis to identify AML somatic mutations using the whole-exome sequencing data of 36 tumor-normal sample pairs from Korean patients with de novo AML. We explored the functional impact of the genes identified in the mutational analyses through an integrated Gene Ontology (GO) and pathway analysis.
RESULTS: A total of 11 genes, including NEFH (p = 6.27 × 10(-13) and q = 1.18 × 10(-8)) and TMPRSS13 (p = 1.40 × 10(-10) and q = 1.32 × 10(-6)), also demonstrated q values less than 0.1 in 36 Korean AML patients. Five out of the 11 novel genes have previously been reported to be associated with other cancers. Two gene mutations, CEBPA (p = 5.22 × 10(-5)) and ATXN3 (p = 9.75 × 10(-4)), showed statistical significance exclusively in the M2 and M3 subtypes of the French-American-British classifications, respectively. A total of 501 genes harbored 478 missense, 22 nonsense, 93 frameshift indels, and/or three stop codon deletions and these gene mutations significantly enriched GO terms for signal transduction (GO:0007165, p = 1.77 × 10(-3)), plasma membrane (GO:0005886, p = 3.07 × 10(-4)), and scaffold protein binding (GO:0097110, p = 8.65 × 10(-4)). The mitogen-activated protein kinase (hsa04010, 7.67 × 10(-4)) was the most enriched Kyoto Encyclopedia of Genes and Genomes pathway.
CONCLUSIONS: Morphological AML subtypes may in part reflect subtype specific patterns of genomic alterations. Following validation, future studies to evaluate the usefulness of these genes in genetic testing for the early diagnosis and prognostic prediction of AML patients would be worthwhile.

PMID: 28249600 [PubMed - indexed for MEDLINE]

Identification of novel candidate variants including COL6A6 polymorphisms in early-onset atopic dermatitis using whole-exome sequencing.

BMC Med Genet. 2017 Jan 26;18(1):8

Authors: Heo WI, Park KY, Jin T, Lee MK, Kim M, Choi EH, Kim HS, Bae JM, Moon NJ, Seo SJ

Abstract
BACKGROUND: The prevalence of atopic dermatitis has increased over the last 10 years. Atopic dermatitis tends to run in families and commonly begins to manifest in childhood. The prevalence of atopic dermatitis is as high as 20% in children. Thus, early diagnosis and treatment of atopic dermatitis are important. Understanding its genetic basis is also needed to facilitate early detection.
METHODS: To identify family-specific candidate genetic variants associated with early-onset atopic dermatitis in Koreans, we carried out whole-exome sequencing of three separate families with this condition. Additional validation was performed in 112 AD patients and 61 controls using Sanger sequencing.
RESULTS: We focused on both common functional variants with a minor allele frequency higher than 1% and rare variants with a minor allele frequency less than 1%. The relevance of the respective variants was supported by a program that could predict whether the mutations resulted in damaged protein function. Fourteen overlapping genes were identified during exome sequencing. Three variants of the COL6A6 gene appeared in all three families and were in close proximity to atopic dermatitis-related loci on chromosome 3q21. The homozygous frequency for the rs16830494 minor allele (AA) and the rs59021909 (TT) allele and the rs200963433 heterozygous (CT) frequency were all higher in AD cases compared to controls in a population-based case-control study.
CONCLUSION: Identifying family-specific COL6A6 polymorphisms and genetic variants of other candidate genes associated with AD using WES is a novel approach. Our study suggests that COL6A6 variants may be risk factors for atopic dermatitis. This study provides a genetic basis for early-onset AD diagnosis in Korean patients and the development of new therapies.
TRIAL REGISTRATION: Trial registration number: IRB NO. C2008030 (133); Name of registry: The collection research of clinical data and patient blood to identify genetic and protein biomarker of atopic dermatitis; Date of registration: 09-July-2008.
TRIAL REGISTRATION NUMBER: IRB NO. C2015258 (1716); Name of registry: The collection study of patient blood and clinical data for the development of the prognosis prediction and early diagnosis of atopic dermatitis; Date of registration: 15-jan-2016.

PMID: 28125976 [PubMed - indexed for MEDLINE]

Identification of a de novo variant in CHUK in a patient with an EEC/AEC syndrome-like phenotype and hypogammaglobulinemia.

Am J Med Genet A. 2017 May 17;:

Authors: Khandelwal KD, Ockeloen CW, Venselaar H, Boulanger C, Brichard B, Sokal E, Pfundt R, Rinne T, van Beusekom E, Bloemen M, Vriend G, Revencu N, Carels CEL, van Bokhoven H, Zhou H

Abstract
The cardinal features of Ectrodactyly, Ectodermal dysplasia, Cleft lip/palate (EEC), and Ankyloblepharon-Ectodermal defects-Cleft lip/palate (AEC) syndromes are ectodermal dysplasia (ED), orofacial clefting, and limb anomalies. EEC and AEC are caused by heterozygous mutations in the transcription factor p63 encoded by TP63. Here, we report a patient with an EEC/AEC syndrome-like phenotype, including ankyloblepharon, ED, cleft palate, ectrodactyly, syndactyly, additional hypogammaglobulinemia, and growth delay. Neither pathogenic mutations in TP63 nor CNVs at the TP63 locus were identified. Exome sequencing revealed de novo heterozygous variants in CHUK (conserved helix-loop-helix ubiquitous kinase), PTGER4, and IFIT2. While the variant in PTGER4 might contribute to the immunodeficiency and growth delay, the variant in CHUK appeared to be most relevant for the EEC/AEC-like phenotype. CHUK is a direct target gene of p63 and encodes a component of the IKK complex that plays a key role in NF-κB pathway activation. The identified CHUK variant (g.101980394T>C; c.425A>G; p.His142Arg) is located in the kinase domain which is responsible for the phosphorylation activity of the protein. The variant may affect CHUK function and thus contribute to the disease phenotype in three ways: (1) the variant exhibits a dominant negative effect and results in an inactive IKK complex that affects the canonical NF-κB pathway; (2) it affects the feedback loop of the canonical and non-canonical NF-κB pathways that are CHUK kinase activity-dependent; and (3) it disrupts NF-κB independent epidermal development that is often p63-dependent. Therefore, we propose that the heterozygous CHUK variant is highly likely to be causative to the EEC/AEC-like and additional hypogammaglobulinemia phenotypes in the patient presented here.

PMID: 28513979 [PubMed - as supplied by publisher]

Exome sequencing of two Italian pedigrees with non-isolated Chiari malformation type I reveals candidate genes for cranio-facial development.

Eur J Hum Genet. 2017 May 17;:

Authors: Merello E, Tattini L, Magi A, Accogli A, Piatelli G, Pavanello M, Tortora D, Cama A, Kibar Z, Capra V, De Marco P

Abstract
Chiari malformation type I (CMI) is a congenital abnormality of the cranio-cerebral junction with an estimated incidence of 1 in 1280. CMI is characterized by underdevelopment of the occipital bone and posterior fossa (PF) and consequent cerebellar tonsil herniation. The presence for a genetic basis to CMI is supported by many lines of evidence. The cellular and molecular mechanisms leading to CM1 are poorly understood. The occipital bone formation is dependent on complex interactions between genes and molecules with pathologies resulting from disruption of this delicate process. Whole-exome sequencing of affected and not affected individuals from two Italian families with non-isolated CMI was undertaken. Single-nucleotide and short insertion-deletion variants were prioritized using KGGSeq knowledge-based platform. We identified three heterozygous missense variants: DKK1 c.121G>A (p.(A41T)) in the first family, and the LRP4 c.2552C>G (p.(T851R)) and BMP1 c.941G>A (p.(R314H)) in the second family. The variants were located at highly conserved residues, segregated with the disease, but they were not observed in 100 unaffected in-house controls. DKK1 encodes for a potent soluble WNT inhibitor that binds to LRP5 and LRP6, and is itself regulated by bone morphogenetic proteins (BMPs). DKK1 is required for embryonic head development and patterning. LRP4 is a novel osteoblast expressed receptor for DKK1 and a WNT and BMP 4 pathways integrator. Screening of DKK1 in a cohort of 65 CMI sporadic patients identified another missense variant, the c.359G>T (p.(R120L)), in two unrelated patients. These findings implicated the WNT signaling in the correct development of the cranial mesenchyme originating the PF.European Journal of Human Genetics advance online publication, 17 May 2017; doi:10.1038/ejhg.2017.71.

PMID: 28513615 [PubMed - as supplied by publisher]

Haploinsufficiency of ZNF462 is associated with craniofacial anomalies, corpus callosum dysgenesis, ptosis, and developmental delay.

Eur J Hum Genet. 2017 May 17;:

Authors: Weiss K, Wigby K, Fannemel M, Henderson LB, Beck N, Ghali N, Study DDD, Anderlid BM, Lundin J, Hamosh A, Jones MC, Ghedia S, Muenke M, Kruszka P

Abstract
The introduction of whole-exome sequencing into the Pediatric Genetics clinic has increased the identification of novel genes associated with neurodevelopmental disorders and congenital anomalies. This agnostic approach has shed light on multiple proteins and pathways not previously known to be associated with disease. Here we report eight subjects from six families with predicted loss of function variants in ZNF462, a zinc-finger protein of unknown function. These individuals have overlapping phenotypes that include ptosis, metopic ridging, craniosynostosis, dysgenesis of the corpus callosum, and developmental delay. We propose that ZNF462 plays an important role in embryonic development, and is associated with craniofacial and neurodevelopmental abnormalities.European Journal of Human Genetics advance online publication, 17 May 2017; doi:10.1038/ejhg.2017.86.

PMID: 28513610 [PubMed - as supplied by publisher]

CAGI4 Crohn's exome challenge: Marker SNP versus exome variant models for assigning risk of Crohn disease.

Hum Mutat. 2017 May 16;:

Authors: Pal LR, Kundu K, Yin Y, Moult J

Abstract
Understanding the basis of complex trait disease is a fundamental problem in human genetics. The CAGI Crohn's Exome challenges are providing insight into the adequacy of current disease models by requiring participants to identify which of a set of individuals has been diagnosed with the disease, given exome data. For the CAGI4 round, we developed a method that used the genotypes from exome sequencing data only to impute the status of Genome Wide Association Studies (GWAS) marker single nucleotide polymorphisms (SNPs). We then used the imputed genotypes as input to several machine learning methods that had been trained to predict disease status from marker SNP information. We achieved the best performance using Naïve Bayes and with a consensus machine learning method, obtaining an area under the curve (AUC) of 0.72, larger than other methods used in CAGI4. We also developed a model that incorporated the contribution from rare missense variants in the exome data, but this performed less well. Future progress is expected to come from the use of whole genome data rather than exomes. This article is protected by copyright. All rights reserved.

PMID: 28512778 [PubMed - as supplied by publisher]

Mutation screening in genes known to be responsible for Retinitis Pigmentosa in 98 Small Han Chinese Families.

Sci Rep. 2017 May 16;7(1):1948

Authors: Huang L, Zhang Q, Huang X, Qu C, Ma S, Mao Y, Yang J, Li Y, Li Y, Tan C, Zhao P, Yang Z

Abstract
Retinitis pigmentosa (RP) is highly heterogeneous in both clinical and genetic fields. Accurate mutation screening is very beneficial in improving clinical diagnosis and gene-specific treatment of RP patients. The reason for the difficulties in genetic diagnosis of RP is that the ethnic-specific mutation databases that contain both clinical and genetic information are largely insufficient. In this study, we recruited 98 small Han Chinese families clinically diagnosed as RP, including of 22 dominant, 19 recessive, 52 sporadic, and five X-linked. We then used whole exome sequencing (WES) analysis to detect mutations in the genes known for RP in 101 samples from these 98 families. In total, we identified 57 potential pathogenic mutations in 40 of the 98 (41%) families in 22 known RP genes, including 45 novel mutations. We detected mutations in 13 of the 22 (59%) typical autosomal dominant families, 8 of the 19 (42%) typical autosomal recessive families, 16 of the 52 (31%) sporadic small families, and four of the five (80%) X-linked families. Our results extended the mutation spectrum of known RP genes in Han Chinese, thus making a contribution to RP gene diagnosis and the pathogenetic study of RP genes.

PMID: 28512305 [PubMed - in process]

Obscurin variants and inherited cardiomyopathies.

Biophys Rev. 2017 May 05;:

Authors: Marston S

Abstract
The inherited cardiomyopathies, hypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM) and left ventricular non-compaction (LVNC), have been frequently associated with mutations in sarcomeric proteins. In recent years, advances in DNA sequencing technology has allowed the study of the giant proteins of the sarcomere, such as titin and nebulin. Obscurin has been somewhat neglected in these studies, largely because its functional role is far from clear, although there was an isolated report in 2007 of obscurin mutations associated with HCM. Recently, whole exome sequencing methodology (WES) has been used to address mutations in OBSCN, the gene for obscurin, and OBSCN variants were found to be relatively common in inherited cardiomyopathies. In different studies, 5 OBSCN unique variants have been found in a group of 30 end-stage failing hearts, 6 OBSCN unique variants in 74 HCM cases and 3 OBSCN unique variants in 10 LVNC patients. As yet, the number of known potentially disease-causing OBSCN variants is quite small. The reason for this is that mutations in the OBSCN gene have not been recognised as potentially disease-causing until recently, and were not included in large-scale genetic surveys. OBSCN mutations may be causative of HCM, DCM and LVNC and other cardiomyopathies, or they may work in concert with other variants in the same or other genes to initiate the pathology. Currently, the function of obscurin is not well understood, but we anticipate that many more OBSCN variants linked to cardiomyopathy will be found when the large cohorts of patient sequences available are tested. It is to be hoped that the establishment of the importance of obscurin in pathology will stimulate a thorough investigation of obscurin function.

PMID: 28510120 [PubMed - as supplied by publisher]

Whole-Exome Sequencing Identifies a Novel Homozygous Frameshift Mutation in the MTMR2 Gene as a Causative Mutation in a Patient with Charcot-Marie-Tooth Disease Type 4B1.

Mol Neurobiol. 2017 May 16;:

Authors: Abdalla-Moady T, Peleg A, Sadeh O, Badarneh K, Fares F

Abstract
Charcot-Marie-Tooth (CMT) disease refers to a heterogeneous group of axonal and demyelinating polyneuropathies, characterized by chronic motor and sensory dysfunction. CMT is the most common genetic cause of neuropathy. The present study aimed to identify the gene mutation responsible for CMT in Ashkenazi Jew (AJ) patient. Genomic DNA was extracted from whole blood leukocytes of affected family and normal subject. Whole-exome sequencing was performed using the Illumina HiSeq2500. The DNA region containing the identified mutation was amplified by PCR and sequenced using dye-terminator chemistry and the forward primer. Physical examination of the patient revealed weakness and atrophy of the lower extremity muscles and Pes cavus foot deformity. Whole-exome sequencing indicated that the patient is homozygous for a novel frameshift mutation (c.1877_1878insAGAG, p.Arg630fs) in the myotubularin-related protein-2 gene (MTMR2), which resulted in an erroneous C-terminal sequence and extension by 15 amino acids. Patients' parents are healthy, and DNA sequencing analysis indicated that both are heterozygotes to the described mutation. The clinical feature of the patient may indicate a complete co-segregation of the p.Arg630fs mutation in MTMR2 gene with the CMT type 4B1 phenotype. Further studies are needed in order to estimate the prevalence of this mutation among AJ.

PMID: 28509084 [PubMed - as supplied by publisher]

Protein Truncating Variants at the Cholesteryl Ester Transfer Protein Gene and Risk for Coronary Heart Disease.

Circ Res. 2017 May 15;:

Authors: Nomura A, Won HH, Khera AV, Takeuchi F, Ito K, McCarthy S, Emdin CA, Klarin D, Natarajan P, Zekavat SM, Gupta N, Peloso GM, Borecki IB, Teslovich TM, Asselta R, Duga S, Merlini PA, Correa A, Kessler T, Wilson JG, Bown MJ, Hall AS, Braund PS, Carey DJ, Murray MF, Kirchner HL, Leader JB, Lavage DR, Manus JN, Hartzel DN, Samani NJ, Schunkert H, Marrugat J, Elosua R, McPherson R, Farrall M, Watkins H, Juang JJ, Hsiung CA, Lin SY, Wang JS, Tada H, Kawashiri MA, Inazu A, Yamagishi M, Katsuya T, Nakashima E, Nakatochi M, Yamamoto K, Yokota M, Momozawa Y, Rotter JI, Lander ES, Rader DJ, Danesh JN, Ardissino D, Gabriel SB, Willer CJ, Abecasis G, Saleheen D, Kubo M, Kato N, Chen YI, Dewey F, Kathiresan S

Abstract
Rationale: Therapies which inhibit cholesteryl ester transfer protein (CETP) have failed to demonstrate a reduction in risk for coronary heart disease (CHD). Human deoxyribonucleic acid sequence variants that truncate the CETP gene may provide insight into the efficacy of CETP inhibition. Objective: To test whether protein truncating variants (PTVs) at the CETP gene were associated with plasma lipid levels and CHD. Methods and Results: We sequenced the exons of the CETP gene in 58,469 participants from 12 case-control studies (18,817 CHD cases, 39,652 CHD-free controls). We defined PTV as those that lead to a premature stop, disrupt canonical splice-sites, or lead to insertions/deletions that shift frame. We also genotyped one Japanese-specific PTV in 27,561 participants from three case-control studies (14,286 CHD cases, 13,275 CHD-free controls). We tested association of CETP PTV carrier status with both plasma lipids and CHD. Among 58,469 participants with CETP gene sequencing data available, average age was 51.5 years and 43% were female; 1 in 975 participants carried a PTV at the CETP gene. Compared to non-carriers, carriers of PTV at CETP had higher high-density lipoprotein cholesterol (HDL-C; effect size, 22.6 mg/dL; 95% confidence interval [CI], 18 to 27; P < 1.0x10(-4)), lower low-density lipoprotein cholesterol (LDL-C; -12.2 mg/dL; 95% CI, -23 to -0.98; P = 0.033), and lower triglycerides (-6.3%; 95% CI, -12 to -0.22, P = 0.043). CETP PTV carrier status was associated with reduced risk for CHD (summary odds ratio, 0.70; 95% CI, 0.54 to 0.90; P = 5.1x10-3). Conclusions: Compared with non-carriers, carriers of PTV at CETP displayed higher HDL-C, lower LDL-C, lower triglycerides, and lower risk for CHD.

PMID: 28506971 [PubMed - as supplied by publisher]

RXRB is a MHC-encoded susceptibility gene associated with anti-topoisomerase I antibody-positive systemic sclerosis.

J Invest Dermatol. 2017 May 12;:

Authors: Oka A, Asano Y, Hasegawa M, Fujimoto M, Ishikawa O, Kuwana M, Kawaguchi Y, Yamamoto T, Takahashi H, Goto D, Endo H, Jinnin M, Mano S, Hosomichi K, Mabuchi T, Ueda MT, Nakagawa S, Beck S, Bahram S, Takehara K, Sato S, Ihn H

Abstract
Systemic sclerosis (SSc) is a systemic autoimmune and connective tissue disorder associated with the human leukocyte antigen (HLA) locus. However, the functional relationship between HLA gene(s) and disease development remains unknown. To elucidate major histocompatibility complex (MHC)-linked SSc genetics, we performed genotyping of MHC-borne microsatellites and HLA-DPB1 alleles using DNA obtained from 318 anti-topoisomerase I antibody-positive patients and 561 healthy controls, all of Japanese descent. Those results revealed 2 MHC haplotypes associated with SSc. Exome sequencing and targeted analysis of these risk haplotypes identified rs17847931 in retinoid X receptor beta (RXRB) as a susceptibility variant (P=1.3×10(-15); odds ratio (OR)=9.4) with amino acid substitution p.V95A on the risk haplotype harboring HLA-DPB1*13:01. No identical variant in the other haplotype including DPB1*09:01 was observed, though that haplotype also showed a significant association (P=8.5×10(-22); OR =4.3) with SSc. Furthermore, the number of risk factors was shown to be a predominant factor, as individuals with 2 factors had elevated risk (P=6.7 × 10(-13); OR=30.2). We concluded that RXRB may be involved in anti-fibrotic activity in skin and chromatin remodeling.

PMID: 28506627 [PubMed - as supplied by publisher]

New mutations in non-syndromic primary ovarian insufficiency patients identified via whole-exome sequencing.

Hum Reprod. 2017 May 13;:1-9

Authors: Patiño LC, Beau I, Carlosama C, Buitrago JC, González R, Suárez CF, Patarroyo MA, Delemer B, Young J, Binart N, Laissue P

Abstract
STUDY QUESTION: Is it possible to identify new mutations potentially associated with non-syndromic primary ovarian insufficiency (POI) via whole-exome sequencing (WES)?
SUMMARY ANSWER: WES is an efficient tool to study genetic causes of POI as we have identified new mutations, some of which lead to protein destablization potentially contributing to the disease etiology.
WHAT IS KNOWN ALREADY: POI is a frequently occurring complex pathology leading to infertility. Mutations in only few candidate genes, mainly identified by Sanger sequencing, have been definitively related to the pathogenesis of the disease.
STUDY DESIGN, SIZE, DURATION: This is a retrospective cohort study performed on 69 women affected by POI.
PARTICIPANTS/MATERIALS, SETTING, METHODS: WES and an innovative bioinformatics analysis were used on non-synonymous sequence variants in a subset of 420 selected POI candidate genes. Mutations in BMPR1B and GREM1 were modeled by using fragment molecular orbital analysis.
MAIN RESULTS AND THE ROLE OF CHANCE: Fifty-five coding variants in 49 genes potentially related to POI were identified in 33 out of 69 patients (48%). These genes participate in key biological processes in the ovary, such as meiosis, follicular development, granulosa cell differentiation/proliferation and ovulation. The presence of at least two mutations in distinct genes in 42% of the patients argued in favor of a polygenic nature of POI.
LIMITATIONS, REASONS FOR CAUTION: It is possible that regulatory regions, not analyzed in the present study, carry further variants related to POI.
WIDER IMPLICATIONS OF THE FINDINGS: WES and the in silico analyses presented here represent an efficient approach for mapping variants associated with POI etiology. Sequence variants presented here represents potential future genetic biomarkers.
STUDY FUNDING/COMPETING INTEREST(S): This study was supported by the Universidad del Rosario and Colciencias (Grants CS/CIGGUR-ABN062-2016 and 672-2014). Colciencias supported Liliana Catherine Patiño´s work (Fellowship: 617, 2013). The authors declare no conflict of interest.

PMID: 28505269 [PubMed - as supplied by publisher]

Whole exome sequencing of a consanguineous family identifies the possible modifying effect of a globally rare AK5 allelic variant in celiac disease development among Saudi patients.

PLoS One. 2017;12(5):e0176664

Authors: Al-Aama JY, Shaik NA, Banaganapalli B, Salama MA, Rashidi O, Sahly AN, Mohsen MO, Shawoosh HA, Shalabi HA, Edreesi MA, Alharthi SE, Wang J, Elango R, Saadah OI

Abstract
Celiac disease (CD), a multi-factorial auto-inflammatory disease of the small intestine, is known to occur in both sporadic and familial forms. Together HLA and Non-HLA genes can explain up to 50% of CD's heritability. In order to discover the missing heritability due to rare variants, we have exome sequenced a consanguineous Saudi family presenting CD in an autosomal recessive (AR) pattern. We have identified a rare homozygous insertion c.1683_1684insATT, in the conserved coding region of AK5 gene that showed classical AR model segregation in this family. Sequence validation of 200 chromosomes each of sporadic CD cases and controls, revealed that this extremely rare (EXac MAF 0.000008) mutation is highly penetrant among general Saudi populations (MAF is 0.62). Genotype and allelic distribution analysis have indicated that this AK5 (c.1683_1684insATT) mutation is negatively selected among patient groups and positively selected in the control group, in whom it may modify the risk against CD development [p<0.002]. Our observation gains additional support from computational analysis which predicted that Iso561 insertion shifts the existing H-bonds between 400th and 556th amino acid residues lying near the functional domain of adenylate kinase. This shuffling of amino acids and their H-bond interactions is likely to disturb the secondary structure orientation of the polypeptide and induces the gain-of-function in nucleoside phosphate kinase activity of AK5, which may eventually down-regulates the reactivity potential of CD4+ T-cells against gluten antigens. Our study underlines the need to have population-specific genome databases to avoid false leads and to identify true candidate causal genes for the familial form of celiac disease.

PMID: 28505210 [PubMed - in process]

Further Validation of the SIGMAR1 c.151+1G>T Mutation as Cause of Distal Hereditary Motor Neuropathy.

Child Neurol Open. 2016 Jan-Dec;3:2329048X16669912

Authors: Lee JJY, van Karnebeek CDM, Drögemoller B, Shyr C, Tarailo-Graovac M, Eydoux P, Ross CJ, Wasserman WW, Björnson B, Wu JK

Abstract
Distal hereditary motor neuropathies represent a group of rare genetic disorders characterized by progressive distal motor weakness without sensory loss. Their genetic heterogeneity is high and thus eligible for diagnostic whole exome sequencing. The authors report successful application of whole exome sequencing in diagnosing a second consanguineous family with distal hereditary motor neuropathy due to a homozygous c.151+1G>T variant in SIGMAR1. This variant was recently proposed as causal for the same condition in a consanguineous Chinese family. Compared to this family, the Afghan ethnic origin of our patient is distinct, yet the features are identical, validating the SIGMAR1 deficiency phenotype: progressive muscle wasting/weakness in lower and upper limbs without sensory loss. Rapid disease progression during adolescent growth is similar and may be due to SIGMAR1's role in regulating axon elongation and tau phosphorylation. Finally, the authors conclude that SIGMAR1 deficiency should be added to the differential diagnosis of distal hereditary motor neuropathies.

PMID: 28503617 [PubMed - in process]

A case of a novel mutation in HNF1β-related maturity-onset diabetes of the young type 5 with diabetic kidney disease complication in a Chinese family.

J Diabetes Complications. 2016 Nov 15;:

Authors: Wang Y, Zhao Y, Zhang J, Yang Y, Liu F

Abstract
AIMS: Precise diagnosis of maturity-onset diabetes of the young (MODY) has proven valuable for understanding mechanism of diabetes and selecting optimal therapy. A proband and her mother with diabetic kidney disease (DKD) were studied to investigate potential genes responsible for diabetes and different severity of DKD between the parent and offspring.
METHODS: The family with suspected MODY underwent mutational analyses by the whole exome sequencing (WES). Candidate pathogenic variants were validated by Sanger sequencing and tested for co-segregation. The clinical parameters of subjects were collected from medical records.
RESULTS: A novel missense heterozygous mutation in exon 4 of the hepatocyte nuclear factor 1β (HNF1β), c.1007A > G (p.H336R), was identified in both the proband and her mother. Moreover, comparing the family's WES results, we found that the proband had acquired a KCNQ1 gene mutation from her father and acquired ACE and SORBS1 gene mutations from her mother. These three genes are known susceptibility genes of DKD and may impose additional effects contributing to DKD severity.
CONCLUSIONS: A novel mutation in HNF1β-MODY was identified in a Chinese family complicated with DKD, and the additional effect of pathogenic variants in susceptibility genes was speculated to contribute to DKD severity.

PMID: 28502589 [PubMed - as supplied by publisher]

Differential analysis of mutations in the Jewish population and their implications for diseases.

Genet Res (Camb). 2017 May 15;99:e3

Authors: Einhorn Y, Weissglas-Volkov D, Carmi S, Ostrer H, Friedman E, Shomron N

Abstract
Sequencing large cohorts of ethnically homogeneous individuals yields genetic insights with implications for the entire population rather than a single individual. In order to evaluate the genetic basis of certain diseases encountered at high frequency in the Ashkenazi Jewish population (AJP), as well as to improve variant annotation among the AJP, we examined the entire exome, focusing on specific genes with known clinical implications in 128 Ashkenazi Jews and compared these data to other non-Jewish populations (European, African, South Asian and East Asian). We targeted American College of Medical Genetics incidental finding recommended genes and the Catalogue of Somatic Mutations in Cancer (COSMIC) germline cancer-related genes. We identified previously known disease-causing variants and discovered potentially deleterious variants in known disease-causing genes that are population specific or substantially more prevalent in the AJP, such as in the ATP and HGFAC genes associated with colorectal cancer and pancreatic cancer, respectively. Additionally, we tested the advantage of utilizing the database of the AJP when assigning pathogenicity to rare variants of independent whole-exome sequencing data of 49 Ashkenazi Jew early-onset breast cancer (BC) patients. Importantly, population-based filtering using our AJP database enabled a reduction in the number of potential causal variants in the BC cohort by 36%. Taken together, population-specific sequencing of the AJP offers valuable, clinically applicable information and improves AJP filter annotation.

PMID: 28502252 [PubMed - in process]