Association of TMTC2 With Human Nonsyndromic Sensorineural Hearing Loss.

JAMA Otolaryngol Head Neck Surg. 2016 Sep 01;142(9):866-72

Authors: Runge CL, Indap A, Zhou Y, Kent JW, King E, Erbe CB, Cole R, Littrell J, Merath K, James R, Rüschendorf F, Kerschner JE, Marth G, Hübner N, Göring HH, Friedland DR, Kwok WM, Olivier M

Abstract
IMPORTANCE: Sensorineural hearing loss (SNHL) is commonly caused by conditions that affect cochlear structures or the auditory nerve, and the genes identified as causing SNHL to date only explain a fraction of the overall genetic risk for this debilitating disorder. It is likely that other genes and mutations also cause SNHL.
OBJECTIVE: To identify a candidate gene that causes bilateral, symmetric, progressive SNHL in a large multigeneration family of Northern European descent.
DESIGN, SETTING, AND PARTICIPANTS: In this prospective genotype and phenotype study performed from January 1, 2006, through April 1, 2016, a 6-generation family of Northern European descent with 19 individuals having reported early-onset hearing loss suggestive of an autosomal dominant inheritance were studied at a tertiary academic medical center. In addition, 179 unrelated adult individuals with SNHL and 186 adult individuals reporting nondeafness were examined.
MAIN OUTCOMES AND MEASURES: Sensorineural hearing loss.
RESULTS: Nine family members (5 women [55.6%]) provided clinical audiometric and medical records that documented hearing loss. The hearing loss is characterized as bilateral, symmetric, progressive SNHL that reached severe to profound loss in childhood. Audiometric configurations demonstrated a characteristic dip at 1000 to 2000 Hz. All affected family members wear hearing aids or have undergone cochlear implantation. Exome sequencing and linkage and association analyses identified a fully penetrant sequence variant (rs35725509) on chromosome 12q21 (logarithm of odds, 3.3) in the TMTC2 gene region that segregates with SNHL in this family. This gene explains the SNHL occurrence in this family. The variant is also associated with SNHL in a cohort of 363 unrelated individuals (179 patients with confirmed SNHL and 184 controls, P = 7 × 10-4).
CONCLUSIONS AND RELEVANCE: A previously uncharacterized gene, TMTC2, has been identified as a candidate for causing progressive SNHL in humans. This finding identifies a novel locus that causes autosomal dominant SNHL and therefore a more detailed understanding of the genetic basis of SNHL. Because TMTC2 has not been previously reported to regulate auditory function, the discovery reveals a potentially new, uncharacterized mechanism of hearing loss.

PMID: 27311106 [PubMed - indexed for MEDLINE]

Identification of partial SLC20A2 deletions in primary brain calcification using whole-exome sequencing.

Eur J Hum Genet. 2016 Nov;24(11):1630-1634

Authors: David S, Ferreira J, Quenez O, Rovelet-Lecrux A, Richard AC, Vérin M, Jurici S, Le Ber I, Boland A, Deleuze JF, Frebourg T, Mendes de Oliveira JR, Hannequin D, Campion D, Nicolas G

Abstract
Primary brain calcification (PBC) is a dominantly inherited calcifying disorder of the brain. SLC20A2 loss-of-function variants account for the majority of families. Only one genomic deletion encompassing SLC20A2 and six other genes has been reported. We performed whole-exome sequencing (WES) in 24 unrelated French patients with PBC, negatively screened for sequence variant in the known genes SLC20A2, PDGFB, PDGFRB and XPR1. We used the CANOES tool to detect copy number variations (CNVs). We detected two deletions of exon 2 of SLC20A2 in two unrelated patients, which segregated with PBC in one family. We then reanalyzed the same series using a QMPSF assay including one amplicon in each exon of SLC20A2 and detected two supplemental partial deletions in two patients: one deletion of exon 4 and one deletion of exons 4 and 5. These deletions were missed by the first screening step of CANOES but could finally be detected after readjustment of bioinformatic parameters and use of a genotyping step of CANOES. This study reports the first partial deletions of SLC20A2 and strengthens its position as the major PBC-causative gene. It is possible to detect short CNVs from WES data, although the sensitivity of such tools should be evaluated in comparison with other methods.

PMID: 27245298 [PubMed - indexed for MEDLINE]

Functional characterization of novel ABCB6 mutations and their clinical implications in familial pseudohyperkalemia.

Haematologica. 2016 Aug;101(8):909-17

Authors: Andolfo I, Russo R, Manna F, De Rosa G, Gambale A, Zouwail S, Detta N, Pardo CL, Alper SL, Brugnara C, Sharma AK, De Franceschi L, Iolascon A

Abstract
Isolated familial pseudohyperkalemia is a dominant red cell trait characterized by cold-induced 'passive leak' of red cell potassium ions into plasma. The causative gene of this condition is ABCB6, which encodes an erythrocyte membrane ABC transporter protein bearing the Langereis blood group antigen system. In this study analyzing three new families, we report the first functional characterization of ABCB6 mutants, including the homozygous mutation V454A, heterozygous mutation R276W, and compound heterozygous mutations R276W and R723Q (in trans). All these mutations are annotated in public databases, suggesting that familial pseudohyperkalemia could be common in the general population. Indeed, we identified variant R276W in one of 327 random blood donors (0.3%). Four weeks' storage of heterozygous R276W blood cells resulted in massive loss of potassium compared to that from healthy control red blood cells. Moreover, measurement of cation flux demonstrated greater loss of potassium or rubidium ions from HEK-293 cells expressing ABCB6 mutants than from cells expressing wild-type ABCB6. The R276W/R723Q mutations elicited greater cellular potassium ion efflux than did the other mutants tested. In conclusion, ABCB6 missense mutations in red blood cells from subjects with familial pseudohyperkalemia show elevated potassium ion efflux. The prevalence of such individuals in the blood donor population is moderate. The fact that storage of blood from these subjects leads to significantly increased levels of potassium in the plasma could have serious clinical implications for neonates and infants receiving large-volume transfusions of whole blood. Genetic tests for familial pseudohyperkalemia could be added to blood donor pre-screening. Further study of ABCB6 function and trafficking could be informative for the study of other pathologies of red blood cell hydration.

PMID: 27151991 [PubMed - indexed for MEDLINE]

Association of NOD2 Mutations with Aggressive Periodontitis.

J Dent Res. 2017 Jun 01;:22034517715432

Authors: Sudo T, Okada Y, Ozaki K, Urayama K, Kanai M, Kobayashi H, Gokyu M, Izumi Y, Tanaka T

Abstract
Aggressive periodontitis (AgP) is characterized by rapid alveolar bone destruction and tooth loss early in life, and its etiology remains unclear. To explore the genetic risk factors of AgP, we performed genome-wide single-nucleotide polymorphism genotyping for identity-by-descent mapping and identified 32 distinct candidate loci, followed by whole exome sequencing with 2 pedigrees of AgP consisting of 3 cases and 1 control in 1 family and 2 sibling cases in the other. After variant filtering procedures and validation by targeted Sanger sequencing, we identified 2 missense mutations at 16q12 in NOD2 (p.Ala110Thr and p.Arg311Trp), which encodes nucleotide-binding oligomerization domain protein 2. We further examined 94 genetically unrelated AgP patients by targeted sequencing of NOD2 and found that 2 patients among them also carried the p.Arg311Trp variant. Furthermore, we found 3 additional missense mutations in this gene (p.His370Tyr, p.Arg459Cys, and p.Ala868Thr). These mutations either had not been previously observed or are extremely rare (frequency <0.001) in Asian populations. NOD2 plays a crucial role in innate immunity as an intracellular receptor initiating nuclear factor κB-dependent and mitogen-activated protein kinase-dependent gene transcription. These results demonstrated NOD2 as a novel gene involved in AgP.

PMID: 28682159 [PubMed - as supplied by publisher]

Targeted exome sequencing of Korean triple-negative breast cancer reveals homozygous deletions associated with poor prognosis of adjuvant chemotherapy-treated patients.

Oncotarget. 2017 Jun 27;:

Authors: Jeong HM, Kim RN, Kwon MJ, Oh E, Han J, Lee SK, Choi JS, Park S, Nam SJ, Gong GY, Nam JW, Choi DH, Lee H, Nam BH, Choi YL, Shin YK

Abstract
Triple-negative breast cancer is characterized by the absence of estrogen and progesterone receptors and human epidermal growth factor receptor 2, and is associated with a poorer outcome than other subtypes of breast cancer. Moreover, there are no accurate prognostic genes or effective therapeutic targets, thereby necessitating continued intensive investigation. This study analyzed the genetic mutation landscape in 70 patients with triple-negative breast cancer by targeted exome sequencing of tumor and matched normal samples. Sequencing showed that more than 50% of these patients had deleterious mutations and homozygous deletions of DNA repair genes, such as ATM, BRCA1, BRCA2, WRN, and CHEK2. These findings suggested that a large number of patients with triple-negative breast cancer have impaired DNA repair function and that therefore a poly ADP-ribose polymerase inhibitor may be an effective drug in the treatment of this disease. Notably, homozygous deletion of three genes, EPHA5, MITF, and ACSL3, was significantly associated with an increased risk of recurrence or distant metastasis in adjuvant chemotherapy-treated patients.

PMID: 28679863 [PubMed - as supplied by publisher]

An unusual genomic variant of pancreatic ductal adenocarcinoma with an indolent clinical course.

Cold Spring Harb Mol Case Stud. 2017 Jul;3(4):

Authors: Kohutek ZA, Rosati LM, Hong J, Poling J, Attiyeh MA, Makohon-Moore A, Herman JM, Iacobuzio-Donahue CA

Abstract
We describe an 85-yr-old male of Ashkenazi Jewish descent with biopsy-proven locally advanced pancreatic ductal adenocarcinoma (PDA). The patient underwent a modified course of gemcitabine and stereotactic body radiation therapy and survived for 42 mo with a stable pancreatic head mass and no evidence of metastatic disease before death due to complications from a stroke. Whole-exome sequencing of his tumor revealed a simple genome landscape with no evidence of mutations, copy-number changes, or structural alterations in genes most commonly associated with PDA (i.e., KRAS, CDKN2A, TP53, or SMAD4). An analysis of his germline DNA revealed no pathogenic variants of significance. Whole-exome and whole-genome sequencing identified a somatic mutation of RNF213 and an inversion/deletion of CTNNA2 as the genetic basis of his PDA. Although PDA is classically characterized by a predictable set of mutations, these data suggest that alternate genetic paths to PDA may exist, which can be associated with a more indolent clinical course.

PMID: 28679692 [PubMed - in process]

Risk Prediction Modeling on Family-Based Sequencing Data Using a Random Field Method.

Genetics. 2017 Jul 05;:

Authors: Wen Y, Burt A, Lu Q

Abstract
Family-based design is one of the most popular designs in genetic studies and has many unique features for risk prediction research. It is more robust against genetic heterogeneity, and the relatedness among family members can be informative for predicting individuals' risk for disease with polygenic and shared environmental components of risk. Despite these strengths, family-based designs have been used infrequently in current risk prediction studies, and their related statistical methods have been much less developed. In this paper, we developed a generalized random field (GRF) method for family-based risk prediction modeling on sequencing data. In GRF, subjects' phenotypes are viewed as stochastic realizations of a random field on a space, and a subject's phenotype is predicted by adjacent subjects, where adjacencies between subjects are determined by their genetic and within-family similarities. Different from existing methods that adjust for familiar correlations, the GRF utilizes this information to form surrogates to further improve prediction accuracy. It also uses within-family information to capture predictors (e.g., rare mutations) that are homogenous in families. Through simulations, we have demonstrated that the GRF method attained better performance than an existing method by considering additional information from family members and accounting for genetic heterogeneity. We further provided practical recommendations for designing family-based risk prediction studies. Finally, we illustrated the GRF method with an application to a whole-genome exome dataset from the Michigan State University Twin Registry study.

PMID: 28679544 [PubMed - as supplied by publisher]

Genetic investigations of the epileptic encephalopathies: Recent advances.

Prog Brain Res. 2016;226:35-60

Authors: Myers CT, Mefford HC

Abstract
The epileptic encephalopathies (EEs) are a group of epilepsy syndromes characterized by multiple seizure types, abundant epileptiform activity, and developmental delay or regression. Advances in genomic technologies over the past decade have accelerated our understanding of the genetic etiology of EE, which is largely due to de novo mutations. Chromosome microarrays to detect copy number variants identify a genomic cause in at least 5-10% of cases. Next-generation sequencing in the form of gene panels or whole exome sequencing have highlighted the role of de novo sequence changes and revealed extensive genetic heterogeneity. The novel gene discoveries in EE implicate diverse cellular pathways including chromatin remodeling, transcriptional regulation, and mTOR regulation in the etiology of epilepsy, highlighting new targets for potential therapeutic intervention. In this chapter, we discuss the rapid pace of gene discovery in EE facilitated by genomic technologies and highlight several novel genes and potential therapies.

PMID: 27323938 [PubMed - indexed for MEDLINE]

Infantile Pain Episodes Associated with Novel Nav1.9 Mutations in Familial Episodic Pain Syndrome in Japanese Families.

PLoS One. 2016;11(5):e0154827

Authors: Okuda H, Noguchi A, Kobayashi H, Kondo D, Harada KH, Youssefian S, Shioi H, Kabata R, Domon Y, Kubota K, Kitano Y, Takayama Y, Hitomi T, Ohno K, Saito Y, Asano T, Tominaga M, Takahashi T, Koizumi A

Abstract
Painful peripheral neuropathy has been correlated with various voltage-gated sodium channel mutations in sensory neurons. Recently Nav1.9, a voltage-gated sodium channel subtype, has been established as a genetic influence for certain peripheral pain syndromes. In this study, we performed a genetic study in six unrelated multigenerational Japanese families with episodic pain syndrome. Affected participants (n = 23) were characterized by infantile recurrent pain episodes with spontaneous mitigation around adolescence. This unique phenotype was inherited in an autosomal-dominant mode. Linkage analysis was performed for two families with 12 affected and nine unaffected members, and a single locus was identified on 3p22 (LOD score 4.32). Exome analysis (n = 14) was performed for affected and unaffected members in these two families and an additional family. Two missense variants were identified: R222H and R222S in SCN11A. Next, we generated a knock-in mouse model harboring one of the mutations (R222S). Behavioral tests (Hargreaves test and cold plate test) using R222S and wild-type C57BL/6 (WT) mice, young (8-9 weeks old; n = 10-12 for each group) and mature (36-38 weeks old; n = 5-6 for each group), showed that R222S mice were significantly (p < 0.05) more hypersensitive to hot and cold stimuli than WT mice. Electrophysiological studies using dorsal root ganglion neurons from 8-9-week-old mice showed no significant difference in resting membrane potential, but input impedance and firing frequency of evoked action potentials were significantly increased in R222S mice compared with WT mice. However, there was no significant difference among Nav1.9 (WT, R222S, and R222H)-overexpressing ND7/23 cell lines. These results suggest that our novel mutation is a gain-of-function mutation that causes infantile familial episodic pain. The mouse model developed here will be useful for drug screening for familial episodic pain syndrome associated with SCN11A mutations.

PMID: 27224030 [PubMed - indexed for MEDLINE]

Multiregional Radiogenomic Assessment of Prostate Microenvironments with Multiparametric MR Imaging and DNA Whole-Exome Sequencing of Prostate Glands with Adenocarcinoma.

Radiology. 2017 Jul;284(1):109-119

Authors: Jamshidi N, Margolis DJ, Raman S, Huang J, Reiter RE, Kuo MD

Abstract
Purpose To assess the underlying genomic variation of prostate gland microenvironments of patients with prostate adenocarcinoma in the context of colocalized multiparametric magnetic resonance (MR) imaging and histopathologic assessment of normal and abnormal regions by using whole-exome sequencing. Materials and Methods Six patients with prostate adenocarcinoma who underwent robotic prostatectomy with whole-mount preservation of the prostate were identified, which enabled spatial mapping between preoperative multiparametric MR imaging and the gland. Four regions of interest were identified within each gland, including regions found to be normal and abnormal via histopathologic analysis. Whole-exome DNA sequencing (>50 times coverage) was performed on each of these spatially targeted regions. Radiogenomic analysis of imaging and mutation data were performed with hierarchical clustering, phylogenetic analysis, and principal component analysis. Results Radiogenomic multiparametric MR imaging and whole-exome spatial characterization in six patients with prostate adenocarcinoma (three patients, Gleason score of 3 + 4; and three patients, Gleason score of 4 + 5) was performed across 23 spatially distinct regions. Hierarchical clustering separated histopathologic analysis-proven high-grade lesions from the normal regions, and this reflected concordance between multiparametric MR imaging and resultant histopathologic analysis in all patients. Seventy-seven mutations involving 29 cancer-associated genes across the 23 spatially distinct prostate samples were identified. There was no significant difference in mutation load in cancer-associated genes between regions that were proven to be normal via histopathologic analysis (34 mutations per sample ± 19), mildly suspicious via multiparametric MR imaging (37 mutations per sample ± 21), intermediately suspicious via multiparametric MR imaging (31 mutations per sample ± 15), and high-grade cancer (33 mutations per sample ± 18) (P = .30). Principal component analysis resolved samples from different patients and further classified samples (regardless of histopathologic status) from prostate glands with Gleason score 3 + 4 versus 4 + 5 samples. Conclusion Multiregion spatial multiparametric MR imaging and whole-exome radiogenomic analysis of prostate glands with adenocarcinoma shows a continuum of mutations across regions that were found via histologic analysis to be high grade and normal. (©) RSNA, 2017 Online supplemental material is available for this article.

PMID: 28453432 [PubMed - indexed for MEDLINE]

Bainbridge-Ropers syndrome caused by loss-of-function variants in ASXL3: a recognizable condition.

Eur J Hum Genet. 2017 Feb;25(2):183-191

Authors: Kuechler A, Czeschik JC, Graf E, Grasshoff U, Hüffmeier U, Busa T, Beck-Woedl S, Faivre L, Rivière JB, Bader I, Koch J, Reis A, Hehr U, Rittinger O, Sperl W, Haack TB, Wieland T, Engels H, Prokisch H, Strom TM, Lüdecke HJ, Wieczorek D

Abstract
Truncating ASXL3 mutations were first identified in 2013 by Bainbridge et al. as a cause of syndromic intellectual disability in four children with similar phenotypes using whole-exome sequencing. The clinical features - postulated by Bainbridge et al. to be overlapping with Bohring-Opitz syndrome - were developmental delay, severe feeding difficulties, failure to thrive and neurological abnormalities. This condition was included in OMIM as 'Bainbridge-Ropers syndrome' (BRPS, #615485). To date, a total of nine individuals with BRPS have been published in the literature in four reports (Bainbridge et al., Dinwiddie et al, Srivastava et al. and Hori et al.). In this report, we describe six unrelated patients with newly diagnosed heterozygous de novo loss-of-function variants in ASXL3 and concordant clinical features: severe muscular hypotonia with feeding difficulties in infancy, significant motor delay, profound speech impairment, intellectual disability and a characteristic craniofacial phenotype (long face, arched eyebrows with mild synophrys, downslanting palpebral fissures, prominent columella, small alae nasi, high, narrow palate and relatively little facial expression). The majority of key features characteristic for Bohring-Opitz syndrome were absent in our patients (eg, the typical posture of arms, intrauterine growth retardation, microcephaly, trigonocephaly, typical facial gestalt with nevus flammeus of the forehead and exophthalmos). Therefore we emphasize that BRPS syndrome, caused by ASXL3 loss-of-function variants, is a clinically distinct intellectual disability syndrome with a recognizable phenotype distinguishable from that of Bohring-Opitz syndrome.

PMID: 27901041 [PubMed - indexed for MEDLINE]

Targeted Sequencing and Meta-Analysis of Preterm Birth.

PLoS One. 2016;11(5):e0155021

Authors: Uzun A, Schuster J, McGonnigal B, Schorl C, Dewan A, Padbury J

Abstract
Understanding the genetic contribution(s) to the risk of preterm birth may lead to the development of interventions for treatment, prediction and prevention. Twin studies suggest heritability of preterm birth is 36-40%. Large epidemiological analyses support a primary maternal origin for recurrence of preterm birth, with little effect of paternal or fetal genetic factors. We exploited an "extreme phenotype" of preterm birth to leverage the likelihood of genetic discovery. We compared variants identified by targeted sequencing of women with 2-3 generations of preterm birth with term controls without history of preterm birth. We used a meta-genomic, bi-clustering algorithm to identify gene sets coordinately associated with preterm birth. We identified 33 genes including 217 variants from 5 modules that were significantly different between cases and controls. The most frequently identified and connected genes in the exome library were IGF1, ATM and IQGAP2. Likewise, SOS1, RAF1 and AKT3 were most frequent in the haplotype library. Additionally, SERPINB8, AZU1 and WASF3 showed significant differences in abundance of variants in the univariate comparison of cases and controls. The biological processes impacted by these gene sets included: cell motility, migration and locomotion; response to glucocorticoid stimulus; signal transduction; metabolic regulation and control of apoptosis.

PMID: 27163930 [PubMed - indexed for MEDLINE]

Critical Genomic Networks and Vasoreactive Variants in Idiopathic Pulmonary Arterial Hypertension.

Am J Respir Crit Care Med. 2016 Aug 15;194(4):464-75

Authors: Hemnes AR, Zhao M, West J, Newman JH, Rich S, Archer SL, Robbins IM, Blackwell TS, Cogan J, Loyd JE, Zhao Z, Gaskill C, Jetter C, Kropski JA, Majka SM, Austin ED

Abstract
RATIONALE: Idiopathic pulmonary arterial hypertension (IPAH) is usually without an identified genetic cause, despite clinical and molecular similarity to bone morphogenetic protein receptor type 2 mutation-associated heritable pulmonary arterial hypertension (PAH). There is phenotypic heterogeneity in IPAH, with a minority of patients showing long-term improvement with calcium channel-blocker therapy.
OBJECTIVES: We sought to identify gene variants (GVs) underlying IPAH and determine whether GVs differ in vasodilator-responsive IPAH (VR-PAH) versus vasodilator-nonresponsive IPAH (VN-PAH).
METHODS: We performed whole-exome sequencing (WES) on 36 patients with IPAH: 17 with VR-PAH and 19 with VN-PAH. Wnt pathway differences were explored in human lung fibroblasts.
MEASUREMENTS AND MAIN RESULTS: We identified 1,369 genes with 1,580 variants unique to IPAH. We used a gene ontology approach to analyze variants and identified overrepresentation of several pathways, including cytoskeletal function and ion binding. By mapping WES data to prior genome-wide association study data, Wnt pathway genes were highlighted. Using the connectivity map to define genetic differences between VR-PAH and VN-PAH, we found enrichment in vascular smooth muscle cell contraction pathways and greater genetic variation in VR-PAH versus VN-PAH. Using human lung fibroblasts, we found increased stimulated Wnt activity in IPAH versus controls.
CONCLUSIONS: A pathway-based analysis of WES data in IPAH demonstrated multiple rare GVs that converge on key biological pathways, such as cytoskeletal function and Wnt signaling pathway. Vascular smooth muscle contraction-related genes were enriched in VR-PAH, suggesting a potentially different genetic predisposition for VR-PAH. This pathway-based approach may be applied to next-generation sequencing data in other diseases to uncover the contribution of unexpected or multiple GVs to a phenotype.

PMID: 26926454 [PubMed - indexed for MEDLINE]

Two Siblings with a Mutation in CCDC8 Presenting with Mild Short Stature: A Case of 3-M Syndrome.

Horm Res Paediatr. 2017 Jul 04;:

Authors: Liao L, Gan HW, Hwa V, Dattani M, Dauber A

Abstract
BACKGROUND: Short stature can be caused by mutations in a multitude of different genes. 3-M syndrome is a rare growth disorder marked by severe pre- and postnatal growth retardation along with subtle dysmorphic features. There have only been 2 prior reports of mutations in CCDC8 causing 3-M syndrome.
METHODS: Two patients presenting with mild short stature underwent whole exome sequencing. The mutation was confirmed via Sanger sequencing. We compare the clinical characteristics of our 2 patients to patients previously reported with mutations in the same gene.
RESULTS: Exome sequencing identified a homozygous frameshift mutation in CCDC8 in both patients. They presented with a much milder phenotype than previously described patients with the same mutation.
CONCLUSION: In this study, we report a case of 2 sisters with relatively mild short stature who were found via exome sequencing to carry a previously reported homozygous mutation in CCDC8. These patients expand the anthropometric phenotype of 3-M syndrome and demonstrate the power of exome sequencing in the diagnosis of children with short stature. 3-M syndrome should be considered in children with mild skeletal abnormalities, normal/high growth hormone-IGF axis parameters, and normal intelligence.

PMID: 28675896 [PubMed - as supplied by publisher]

PD-1 inhibition in congenital pigment synthesizing metastatic melanoma.

Pediatr Blood Cancer. 2017 Jul 04;:

Authors: Weyand AC, Mody RJ, Rabah RM, Opipari VP

Abstract
A newborn female child was born with a congenital pigment synthesizing melanoma of the scalp. Further workup revealed metastatic disease within the liver, lungs, and left tibia. Whole exome sequencing was performed on multiple samples that revealed one somatic mutation, lysine methyltransferase 2C (KMT2C), at low allelic frequency but no v-Raf murine sarcoma viral oncogene homolog B (BRAF), NF-1 mutation. Programmed death ligand 1 was moderately expressed. Treatment was initiated with the programmed cell death protein 1 inhibitor nivolumab. The patient tolerated this treatment well with minimal toxicity. She is now over a year out from initial diagnosis, continuing on nivolumab, with stable disease.

PMID: 28675691 [PubMed - as supplied by publisher]

Compound heterozygosity for loss-of-function GARS variants results in a multi-system developmental syndrome that includes severe growth retardation.

Hum Mutat. 2017 Jul 04;:

Authors: Oprescu SN, Chepa-Lotrea X, Takase R, Golas G, Markello TC, Adams DR, Toro C, Gropman AL, Hou YM, Malicdan MCV, Gahl WA, Tifft CJ, Antonellis A

Abstract
Aminoacyl-tRNA synthetases (ARSs) are ubiquitously expressed enzymes that ligate amino acids onto tRNA molecules. Genes encoding ARSs have been implicated in myriad dominant and recessive disease phenotypes. Glycyl-tRNA synthetase (GARS) is a bi-functional ARS that charges tRNA(Gly) in the cytoplasm and mitochondria. GARS variants have been associated with dominant Charcot-Marie-Tooth disease but have not been convincingly implicated in recessive phenotypes. Here we describe a patient from the NIH Undiagnosed Diseases Program with a multi-system, developmental phenotype. Whole-exome sequence analysis revealed that the patient is compound heterozygous for one frameshift (p.Glu83Ilefs*6) and one missense (p.Arg310Gln) GARS variant. Using in vitro and in vivo functional studies, we show that both GARS variants cause a loss-of-function effect: the frameshift variant results in depleted protein levels and the missense variant reduces GARS tRNA charging activity. In support of GARS variant pathogenicity, our patient shows striking phenotypic overlap with other patients having ARS-related recessive diseases, including features associated with variants in both cytoplasmic and mitochondrial ARSs; this observation is consistent with the essential function of GARS in both cellular locations. In summary, our clinical, genetic, and functional analyses expand the phenotypic spectrum associated with GARS variants. This article is protected by copyright. All rights reserved.

PMID: 28675565 [PubMed - as supplied by publisher]

Epileptic Encephalopathies as Neurodegenerative Disorders.

Adv Neurobiol. 2017;15:295-315

Authors: Helbig I, von Deimling M, Marsh ED

Abstract
The epileptic encephalopathies are severe and often treatment-resistant conditions that are associated with a progressive disturbance of brain function, resulting in a broad range of neurological and non-neurological comorbidities. The concept of epileptic encephalopathies entails that the encephalopathy aspect of the overall condition is primarily driven by the epileptic activity of the disease, which often manifests as specific and pathological features on the electroencephalogram. Genetic factors in epileptic encephalopathies are increasingly recognized. As of 2016, more than 30 genes have been securely implicated as causative genes for genetic epileptic encephalopathies. Even though the traditional concept of epileptic encephalopathies entails that the progressive disturbance of brain dysfunction is primarily due to the abnormal hypersynchronous activity that underlies the seizure disorders, this strict concept rarely holds true for patients with identified genetic etiologies. More commonly, an underlying genetic etiology is thought to predispose both to the neurodevelopmental comorbidities and to the seizure phenotype with a complex interaction between both. In this chapter, we will elucidate to what extent neurodegeneration rather than epilepsy-related regression is a feature of the common epileptic encephalopathies, drawing parallels between two relatively separate fields of neurogenetic research.

PMID: 28674986 [PubMed - in process]

A Novel Hypokalemic-Alkalotic Salt-Losing Tubulopathy in Patients with CLDN10 Mutations.

J Am Soc Nephrol. 2017 Jul 03;:

Authors: Bongers EMHF, Shelton LM, Milatz S, Verkaart S, Bech AP, Schoots J, Cornelissen EAM, Bleich M, Hoenderop JGJ, Wetzels JFM, Lugtenberg D, Nijenhuis T

Abstract
Mice lacking distal tubular expression of CLDN10, the gene encoding the tight junction protein Claudin-10, show enhanced paracellular magnesium and calcium permeability and reduced sodium permeability in the thick ascending limb (TAL), leading to a urine concentrating defect. However, the function of renal Claudin-10 in humans remains undetermined. We identified and characterized CLDN10 mutations in two patients with a hypokalemic-alkalotic salt-losing nephropathy. The first patient was diagnosed with Bartter syndrome (BS) >30 years ago. At re-evaluation, we observed hypocalciuria and hypercalcemia, suggesting Gitelman syndrome (GS). However, serum magnesium was in the upper normal to hypermagnesemic range, thiazide responsiveness was not blunted, and genetic analyses did not show mutations in genes associated with GS or BS. Whole-exome sequencing revealed compound heterozygous CLDN10 sequence variants [c.446C>G (p.Pro149Arg) and c.465-1G>A (p.Glu157_Tyr192del)]. The patient had reduced urinary concentrating ability, with a preserved aquaporin-2 response to desmopressin and an intact response to furosemide. These findings were not in line with any other known salt-losing nephropathy. Subsequently, we identified a second unrelated patient showing a similar phenotype, in whom we detected compound heterozygous CLDN10 sequence variants [c.446C>G (p.(Pro149Arg) and c.217G>A (p.Asp73Asn)]. Cell surface biotinylation and immunofluorescence experiments in cells expressing the encoded mutants showed that only one mutation caused significant differences in Claudin-10 membrane localization and tight junction strand formation, indicating that these alterations do not fully explain the phenotype. These data suggest that pathogenic CLDN10 mutations affect TAL paracellular ion transport and cause a novel tight junction disease characterized by a non-BS, non-GS autosomal recessive hypokalemic-alkalotic salt-losing phenotype.

PMID: 28674042 [PubMed - as supplied by publisher]

Brain involvement in Charcot-Marie-Tooth disease due to ganglioside-induced differentiation associated-protein 1 mutation.

Neuromuscul Disord. 2017 Jun 07;:

Authors: Al-Ghamdi F, Anselm I, Yang E, Ghosh PS

Abstract
Charcot-Marie-Tooth (CMT) due to ganglioside-induced differentiation associated-protein 1 (GDAP1) gene mutation can be inherited as an autosomal recessive (severe phenotype) or dominant (milder phenotype) disorder. GDAP1 protein, located in the outer mitochondrial membrane, is involved in the mitochondrial fission. Brain imaging abnormalities have not been reported in this condition. We described an 8-year-old boy who had an early onset autosomal recessive neuropathy. Whole exome sequencing revealed compound heterozygous mutations in the GDAP1 gene: c.313_313delA, p.Arg105Glufs*3 - a novel mutation (maternally inherited) and c.358C>T, pR120W - a known pathogenic mutation (paternally inherited). He had abnormal brain MRI findings since infancy localized to the middle cerebellar peduncles and cerebellar white matter with sparing of the supratentorial brain. We speculate that GDAP1 protein due to its widespread distribution and mitochondrial location is responsible for these imaging abnormalities. This report expands the spectrum of brain imaging abnormalities seen in different types of CMT.

PMID: 28673555 [PubMed - as supplied by publisher]

SEQSpark: A Complete Analysis Tool for Large-Scale Rare Variant Association Studies using Whole-Genome and Exome Sequence Data.

Am J Hum Genet. 2017 Jun 27;:

Authors: Zhang D, Zhao L, Li B, He Z, Wang GT, Liu DJ, Leal SM

Abstract
Massively parallel sequencing technologies provide great opportunities for discovering rare susceptibility variants involved in complex disease etiology via large-scale imputation and exome and whole-genome sequence-based association studies. Due to modest effect sizes, large sample sizes of tens to hundreds of thousands of individuals are required for adequately powered studies. Current analytical tools are obsolete when it comes to handling these large datasets. To facilitate the analysis of large-scale sequence-based studies, we developed SEQSpark which implements parallel processing based on Spark to increase the speed and efficiency of performing data quality control, annotation, and association analysis. To demonstrate the versatility and speed of SEQSpark, we analyzed whole-genome sequence data from the UK10K, testing for associations with waist-to-hip ratios. The analysis, which was completed in 1.5 hr, included loading data, annotation, principal component analysis, and single variant and rare variant aggregate association analysis of >9 million variants. For rare variant aggregate analysis, an exome-wide significant association (p < 2.5 × 10(-6)) was observed with CCDC62 (SKAT-O [p = 6.89 × 10(-7)], combined multivariate collapsing [p = 1.48 × 10(-6)], and burden of rare variants [p = 1.48 × 10(-6)]). SEQSpark was also used to analyze 50,000 simulated exomes and it required 1.75 hr for the analysis of a quantitative trait using several rare variant aggregate association methods. Additionally, the performance of SEQSpark was compared to Variant Association Tools and PLINK/SEQ. SEQSpark was always faster and in some situations computation was reduced to a hundredth of the time. SEQSpark will empower large sequence-based epidemiological studies to quickly elucidate genetic variation involved in the etiology of complex traits.

PMID: 28669402 [PubMed - as supplied by publisher]