Evaluation of Gene-Based Family-Based Methods to Detect Novel Genes Associated With Familial Late Onset Alzheimer Disease.

Front Neurosci. 2018;12:209

Authors: Fernández MV, Budde J, Del-Aguila JL, Ibañez L, Deming Y, Harari O, Norton J, Morris JC, Goate AM, NIA-LOAD family study group, NCRAD, Cruchaga C

Abstract
Gene-based tests to study the combined effect of rare variants on a particular phenotype have been widely developed for case-control studies, but their evolution and adaptation for family-based studies, especially studies of complex incomplete families, has been slower. In this study, we have performed a practical examination of all the latest gene-based methods available for family-based study designs using both simulated and real datasets. We examined the performance of several collapsing, variance-component, and transmission disequilibrium tests across eight different software packages and 22 models utilizing a cohort of 285 families (N = 1,235) with late-onset Alzheimer disease (LOAD). After a thorough examination of each of these tests, we propose a methodological approach to identify, with high confidence, genes associated with the tested phenotype and we provide recommendations to select the best software and model for family-based gene-based analyses. Additionally, in our dataset, we identified PTK2B, a GWAS candidate gene for sporadic AD, along with six novel genes (CHRD, CLCN2, HDLBP, CPAMD8, NLRP9, and MAS1L) as candidate genes for familial LOAD.

PMID: 29670507 [PubMed]

An adolescence-onset male leukoencephalopathy with remarkable cerebellar atrophy and novel compound heterozygous AARS2 gene mutations: a case report.

J Hum Genet. 2018 Apr 17;:

Authors: Dong Q, Long L, Chang YY, Lin YJ, Liu M, Lu ZQ

Abstract
Mutations in the mitochondrial alanyl-transfer (t)RNA synthetase 2 (AARS2; OMIM 612035) have been linked to leukoencephalopathy recently. Until now, there have been only 13 cases reported in the literature. Hence, the clinical and genetic characteristics of this disease are not fully understood. Here, we reported an adolescence-onset male leukoencephalopathy patient characterized by progressive limb tremor at the age of 17 years. He had no signs of a cardiomyopathy. Magnetic resonance imaging scanning demonstrated severe cerebellar atrophy and white matter abnormalities involving descending tracts. Focused exome sequencing revealed he had novel compound heterozygous mutations in AARS2 gene (c.2265dupA; p.Arg756fs and c.650C>T; p.Pro217Leu). The patient was diagnosed with AARS2 mutation-related leukodystrophy (AARS2-L). We report a case with novel AARS2 gene mutations with developed striking cerebellar atrophy and leukoencephalopathy, which helps to further understand the clinical and genetic heterogeneity of AARS2-L.

PMID: 29666464 [PubMed - as supplied by publisher]

Correction to: Exome sequencing reveals a novel PLP1 mutation in a Moroccan family with connatal Pelizaeus-Merzbacher disease: a case report.

BMC Pediatr. 2018 Apr 17;18(1):138

Authors: Lyahyai J, Bencheikh BOA, Elalaoui SC, Mansouri M, Boualla L, DIonne-Laporte A, Spiegelman D, Dion PA, Cossette P, Rouleau GA, Sefiani A

Abstract
After publication of the original article [1] it was brought to our attention that author Bouchra Ouled Amar Bencheikh was incorrectly included as Bouchra Oulad Amar Bencheikh.

PMID: 29665810 [PubMed - in process]

Identification of eight genetic variants as novel determinants of dyslipidemia in Japanese by exome-wide association studies.

Oncotarget. 2017 Jun 13;8(24):38950-38961

Authors: Yamada Y, Sakuma J, Takeuchi I, Yasukochi Y, Kato K, Oguri M, Fujimaki T, Horibe H, Muramatsu M, Sawabe M, Fujiwara Y, Taniguchi Y, Obuchi S, Kawai H, Shinkai S, Mori S, Arai T, Tanaka M

Abstract
We have performed exome-wide association studies to identify single nucleotide polymorphisms that influence serum concentrations of triglycerides, high density lipoprotein (HDL)-cholesterol, or low density lipoprotein (LDL)-cholesterol or confer susceptibility to hypertriglyceridemia, hypo-HDL-cholesterolemia, or hyper-LDL-cholesterolemia in Japanese. Exome-wide association studies for serum triglycerides (13,414 subjects), HDL-cholesterol (14,119 subjects), LDL-cholesterol (13,577 subjects), hypertriglyceridemia (4742 cases, 8672 controls), hypo-HDL-cholesterolemia (2646 cases, 11,473 controls), and hyper-LDL-cholesterolemia (4489 cases, 9088 controls) were performed with HumanExome-12 DNA Analysis BeadChip or Infinium Exome-24 BeadChip arrays. Twenty-four, 69, or 32 loci were significantly (P < 1.21 × 10-6) associated with serum triglycerides, HDL-cholesterol, or LDL-cholesterol, respectively, with 13, 16, or 9 of these loci having previously been associated with triglyceride-, HDL-cholesterol-, or LDL-cholesterol-related traits, respectively. Two single nucleotide polymorphisms (rs10790162, rs7350481) were significantly related to both serum triglycerides and hypertriglyceridemia; three polymorphisms (rs146515657, rs147317864, rs12229654) were significantly related to both serum HDL-cholesterol and hypo-HDL-cholesterolemia; and six polymorphisms (rs2853969, rs7771335, rs2071653, rs2269704, rs2269703, rs2269702) were significantly related to both serum LDL-cholesterol and hyper-LDL-cholesterolemia. Among polymorphisms identified in the present study, two polymorphisms (rs146515657, rs147317864) may be novel determinants of hypo-HDL-cholesterolemia, and six polymorphisms (rs2853969, rs7771335, rs2071653, rs2269704, rs2269703, rs2269702) may be new determinants of hyper-LDL-cholesterolemia. In addition, 12, 61, 23, or 3 polymorphisms may be new determinants of the serum triglyceride, HDL-cholesterol, or LDL-cholesterol concentrations or of hyper-LDL-cholesterolemia, respectively.

PMID: 28473662 [PubMed - indexed for MEDLINE]

A novel DNAJB6 mutation causes dominantly inherited distal-onset myopathy and compromises DNAJB6 function.

Clin Genet. 2017 Aug;92(2):150-157

Authors: Tsai PC, Tsai YS, Soong BW, Huang YH, Wu HT, Chen YH, Lin KP, Liao YC, Lee YC

Abstract
BACKGROUND: Mutations in the DNAJB6 gene have been identified as a rare cause of dominantly inherited limb-girdle muscular dystrophy or distal-onset myopathy.
MATERIALS AND METHODS: Exome sequencing was performed to investigate a Taiwanese family with a dominantly inherited distal-onset myopathy. Functional effects of the causal mutation were investigated in vitro.
RESULTS: Exome sequencing of the two affected individuals in this family identified a heterozygous mutation, c.287C>T (p.Pro96Leu) in the DNAJB6 gene, which co-segregated with the myopathy within all 12 family members. Notably, this mutation is novel and localizes within the glycine and phenylalanine-rich (G/F) domain and alters an amino acid residue previously reported with a different mutation. Furthermore, immunofluorescence analyses and filter trap assay demonstrated that the c.287C>T (p.Pro96Leu) mutation possessed a dominant negative effect on the anti-aggregation function of DNAJB6 protein.
CONCLUSION: This study expands the molecular spectrum of DNAJB6 mutations and also emphasizes the pathogenic role of DNAJB6 dysfunction in distal-onset myopathy.

PMID: 28233300 [PubMed - indexed for MEDLINE]

Association of the missense variant p.Arg203Trp in PACS1 as a cause of intellectual disability and seizures.

Clin Genet. 2017 Aug;92(2):221-223

Authors: Stern D, Cho MT, Chikarmane R, Willaert R, Retterer K, Kendall F, Deardorff M, Hopkins S, Bedoukian E, Slavotinek A, Schrier Vergano S, Spangler B, McDonald M, McConkie-Rosell A, Burton BK, Kim KH, Oundjian N, Kronn D, Chandy N, Baskin B, Guillen Sacoto MJ, Wentzensen IM, McLaughlin HM, McKnight D, Chung WK

Abstract
Graphical abstract key: ADHD, attention deficit hyperactivity disorder; ASD, atrial septal defect; DD, developmental delay; EEG, electroencephalogram; Ht, height; ID, intellectual disability; OCD, obsessive-compulsive disorder; OFC, open fontanelle; PDA, patent ductus arteriosis; PFO, patent foramen ovale; VSD, ventricular septal defect; Wt, weight.

PMID: 28111752 [PubMed - indexed for MEDLINE]

Mutations in DYNC2H1, the cytoplasmic dynein 2, heavy chain 1 motor protein gene, cause short-rib polydactyly type I, Saldino-Noonan type.

Clin Genet. 2017 Aug;92(2):158-165

Authors: Badiner N, Taylor SP, Forlenza K, Lachman RS, University of Washington Center for Mendelian Genomics, Bamshad M, Nickerson D, Cohn DH, Krakow D

Abstract
The short-rib polydactyly syndromes (SRPS) are autosomal recessively inherited, genetically heterogeneous skeletal ciliopathies. SRPS phenotypes were historically categorized as types I-IV, with type I first delineated by Saldino and Noonan in 1972. Characteristic findings among all forms of SRP include short horizontal ribs, short limbs and polydactyly. The SRP type I phenotype is characterized by a very small thorax, extreme micromelia, very short, poorly mineralized long bones, and multiple organ system anomalies. To date, the molecular basis of this most severe type of SRP, also known as Saldino-Noonan syndrome, has not been determined. We identified three SRP cases that fit the original phenotypic description of SRP type I. In all three cases, exome sequence analysis revealed compound heterozygosity for mutations in DYNC2H1, which encodes the main component of the retrograde IFT A motor, cytoplasmic dynein 2 heavy chain 1. Thus SRP type I, II, III and asphyxiating thoracic dystrophy (ATD), which also result from DYNC2H1 mutations. Herein we describe the phenotypic features, radiographic findings, and molecular basis of SRP type I.

PMID: 27925158 [PubMed - indexed for MEDLINE]

Mutations in plasmalemma vesicle-associated protein cause severe syndromic protein-losing enteropathy.

J Med Genet. 2018 Apr 16;:

Authors: Broekaert IJ, Becker K, Gottschalk I, Körber F, Dötsch J, Thiele H, Altmüller J, Nürnberg P, Hünseler C, Cirak S

Abstract
BACKGROUND: Protein-losing enteropathy (PLE) is characterised by gastrointestinal protein leakage due to loss of mucosal integrity or lymphatic abnormalities. PLE can manifest as congenital diarrhoea and should be differentiated from other congenital diarrhoeal disorders. Primary PLEs are genetically heterogeneous and the underlying genetic defects are currently emerging.
OBJECTIVES: We report an infant with fatal PLE for whom we aimed to uncover the underlying pathogenic mutation.
METHODS: We performed whole exome sequencing (WES) for the index patient. Variants were classified based on the American College of Medical Genetics and Genomics guidelines. WES results and our detailed clinical description of the patient were compared with the literature.
RESULTS: We discovered a novel homozygous stop mutation (c.988C>T, p.Q330*) in the Plasmalemma Vesicle-Associated Protein (PLVAP) gene in a newborn with fatal PLE, facial dysmorphism, and renal, ocular and cardiac anomalies. The Q330* mutation is predicted to result in complete loss of PLVAP protein expression leading to deletion of the diaphragms of endothelial fenestrae, resulting in plasma protein extravasation and PLE. Recently, another single homozygous stop mutation in PLVAP causing lethal PLE in an infant was reported.
CONCLUSIONS: Our findings validate PLVAP mutations as a cause of syndromic PLE. Prenatal anomalies, severe PLE and syndromic features may guide the diagnosis of this rare disease.

PMID: 29661969 [PubMed - as supplied by publisher]

A novel TEX11 mutation induces azoospermia: a case report of infertile brothers and literature review.

BMC Med Genet. 2018 Apr 16;19(1):63

Authors: Sha Y, Zheng L, Ji Z, Mei L, Ding L, Lin S, Wang X, Yang X, Li P

Abstract
BACKGROUND: Testis-expressed gene 11 (TEX11) is an X-linked gene and essential for meiotic recombination and chromosomal synapsis. TEX11 deficiency causes meiotic arrest and male infertility, and many TEX11 mutations have been found in azoospermic and infertile men.
CASE PRESENTATION: This study reported one novel TEX11 mutation (2653G → T, in exon 29, GenBank accession number, NM_031276) in two brothers with azoospermia. This mutation was firstly screened out by whole-exome sequencing (WES) and further verified by amplifying and sequencing the specific exon 29. Surprisingly, the same exonic missense mutation (W856C) was observed in two brothers but not in their mother. Histological analysis of testicular biopsy from both brothers revealed meiotic arrest and no post-meiotic round spermatids and mature spermatozoa were observed in the seminiferous tubules. TEX11 expression was observed strongly in spermatogonia and weakly in spermatocytes, but not in Sertoli cells and interstitial cells.
CONCLUSIONS: We identified one novel TEX11 mutation in two brothers and summarized the literature regarding TEX11 mutations and male infertility. This study and previous literature indicate that TEX11 mutations are closely associated with male infertility, especially azoospermia, although auxiliary clinical analyses are needed to figure out the causes of male infertility.

PMID: 29661171 [PubMed - in process]

Turning the backbone into an ankylosed concrete-like structure: Case report.

Medicine (Baltimore). 2018 Apr;97(15):e0278

Authors: Kaissi AA, Chehida FB, Grill F, Ganger R, Kircher SG

Abstract
RATIONALE: Progressive restriction of the spinal bio-mechanics is not-uncommon deformity encountered in spine clinics. Congenital spinal fusion as seen in Klippel-Feil-anomaly, progressive non-infectious anterior vertebral fusion, and progressive spinal hyperostosis secondary to ossification of the anterior longitudinal spinal ligament are well delineated and recognized.
PATIENT CONCERNS: A 24-year-old girl has history of osteoporosis since her early childhood, associated with multiple axial and appendicular fractures and scoliosis. Recently she presented with episodes of severe back pain, spinal rigidity/stiffness with total loss of spine biomechanics.
DIAGNOSES: She was provisionally diagnosed as having osteogenesis imperfecta and was investigated for COL1A1/A2 mutations which have been proven to be negative. Autosomal recessive type of osteogenesis imperfecta was proposed as well, no mutations have been encountered. A homozygous for CTSA gene mutation, the gene associated with Galactosialidosis was identified via whole exome sequencing (Next-Generation Sequencing projects) has been identified.
INTERVENTIONS: Early in her life she had a history of frequent fractures of the long bones since she was 4 years which was followed by vertebral fractures at the age of 12 years. She manifested lower serum 25OH-D levels and were associated with lower LS-aBMD Z-scores with higher urinary bone turnover indexes (urinary NTX/Cr).
OUTCOMES: Lysosomal storage diseases (LSD) have a strong correlation with the development of osteoporosis. LSD causes skeletal abnormalities results from a lack of skeletal remodeling and ossification abnormalities owing to abnormal deposition of GAGs (impaired degradation of glycosaminoglycans ) in bone and cartilage. 3D reconstruction CT scan of the spine showed diffuse hyperostosis of almost the entire spine (begins at the level of T4- extending downwards to involve the whole thoraco-lumbar and upper part of the sacrum) with total diffuse fusion of the pedicles, the transverse and articular processes, the laminae and the spinous processes.
LESSONS: This is the first clinical report of adult patient with a history of osteoporosis and fractures with the late diagnosis of Galactosialidosis. Osteogenesis imperfecta (autosomal dominant and recessive) were the first given diagnoses which proven negative. The pathophysiology of the spine ankylosis in our current patient and its correlation with LSD, antiresorptive medications, vitamin D3 and supplemental calcium is not fully understood. Therefore, further studies are needed to elucidate this sort of correlation.

PMID: 29642148 [PubMed - indexed for MEDLINE]

Identification of a novel mutation in FGFR1 gene in patients with Kallmann syndrome by high throughput sequencing.

Syst Biol Reprod Med. 2018 Apr 15;:1-5

Authors: Jin BF, Ji ZY, Su ZY, Mei LB, Huang XJ, Lin SB, Li P, Sha YW

Abstract
Kallmann syndrome (KS) is a rare clinical and genetic heterogeneity disease, which is familial or sporadic. KS is known to have three patterns of inheritance: X linked recessive inheritance, autosomal dominant inheritance and rare autosomal recessive inheritance. Here, we report a sibling pedigree with autosomal dominant inheritance of KS, and we identified a novel heterozygous frameshift mutation c.299_300insCCGCAGACTCCGGCCTCTATGC (p.C101Rfs*17) in FGFR1 gene using whole-exome sequencing (WES). The mutation and affection status were cosegregated. The mutation is not present in the dbSNP, 1000 Genome, ExAC, and gnomAD databases. The discovery of this new mutation in the FGFR1 gene enriches the spectrum of FGFR1 mutations in patients with KS.
ABBREVIATIONS: FGFR1: fibroblast growth factor receptor 1; HH: hypogonadotropic hypogonadism; KS: Kallmann syndrome; MRI: magnetic resonance imaging; WES: whole-exome sequencing.

PMID: 29658329 [PubMed - as supplied by publisher]

Truncating Variants in NAA15 Are Associated with Variable Levels of Intellectual Disability, Autism Spectrum Disorder, and Congenital Anomalies.

Am J Hum Genet. 2018 Apr 09;:

Authors: Cheng H, Dharmadhikari AV, Varland S, Ma N, Domingo D, Kleyner R, Rope AF, Yoon M, Stray-Pedersen A, Posey JE, Crews SR, Eldomery MK, Akdemir ZC, Lewis AM, Sutton VR, Rosenfeld JA, Conboy E, Agre K, Xia F, Walkiewicz M, Longoni M, High FA, van Slegtenhorst MA, Mancini GMS, Finnila CR, van Haeringen A, den Hollander N, Ruivenkamp C, Naidu S, Mahida S, Palmer EE, Murray L, Lim D, Jayakar P, Parker MJ, Giusto S, Stracuzzi E, Romano C, Beighley JS, Bernier RA, Küry S, Nizon M, Corbett MA, Shaw M, Gardner A, Barnett C, Armstrong R, Kassahn KS, Van Dijck A, Vandeweyer G, Kleefstra T, Schieving J, Jongmans MJ, de Vries BBA, Pfundt R, Kerr B, Rojas SK, Boycott KM, Person R, Willaert R, Eichler EE, Kooy RF, Yang Y, Wu JC, Lupski JR, Arnesen T, Cooper GM, Chung WK, Gecz J, Stessman HAF, Meng L, Lyon GJ

Abstract
N-alpha-acetylation is a common co-translational protein modification that is essential for normal cell function in humans. We previously identified the genetic basis of an X-linked infantile lethal Mendelian disorder involving a c.109T>C (p.Ser37Pro) missense variant in NAA10, which encodes the catalytic subunit of the N-terminal acetyltransferase A (NatA) complex. The auxiliary subunit of the NatA complex, NAA15, is the dimeric binding partner for NAA10. Through a genotype-first approach with whole-exome or genome sequencing (WES/WGS) and targeted sequencing analysis, we identified and phenotypically characterized 38 individuals from 33 unrelated families with 25 different de novo or inherited, dominantly acting likely gene disrupting (LGD) variants in NAA15. Clinical features of affected individuals with LGD variants in NAA15 include variable levels of intellectual disability, delayed speech and motor milestones, and autism spectrum disorder. Additionally, mild craniofacial dysmorphology, congenital cardiac anomalies, and seizures are present in some subjects. RNA analysis in cell lines from two individuals showed degradation of the transcripts with LGD variants, probably as a result of nonsense-mediated decay. Functional assays in yeast confirmed a deleterious effect for two of the LGD variants in NAA15. Further supporting a mechanism of haploinsufficiency, individuals with copy-number variant (CNV) deletions involving NAA15 and surrounding genes can present with mild intellectual disability, mild dysmorphic features, motor delays, and decreased growth. We propose that defects in NatA-mediated N-terminal acetylation (NTA) lead to variable levels of neurodevelopmental disorders in humans, supporting the importance of the NatA complex in normal human development.

PMID: 29656860 [PubMed - as supplied by publisher]

A rare variant in MLKL confers susceptibility to ApoE ɛ4-negative Alzheimer's disease in Hong Kong Chinese population.

Neurobiol Aging. 2018 Mar 10;:

Authors: Wang B, Bao S, Zhang Z, Zhou X, Wang J, Fan Y, Zhang Y, Li Y, Chen L, Jia Y, Li J, Li M, Zheng W, Mu N, Wang L, Yu Z, Wong DSM, Zhang Y, Kwan J, Ka-Fung Mak H, Ambalavanan A, Zhou S, Cai W, Zheng J, Huang S, Rouleau GA, Yang W, Rogaeva E, Ma X, St George-Hyslop P, Chu LW, Song YQ

Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorders in the elderly. To identify rare genetic factors other than apolipoprotein E ɛ4 allele (ApoE ɛ4) contributing to the pathogenesis of late-onset AD (LOAD), we conducted a whole-exome analysis of 246 ApoE ɛ4-negative LOAD cases and 172 matched controls in Hong Kong Chinese population. LOAD patients showed a significantly higher burden of rare loss-of-function variants in genes related to immune function than healthy controls. Among the genes involved in immune function, we identified a rare stop-gain variant (p.Q48X) in mixed lineage kinase domain like pseudokinase (MLKL) gene present exclusively in 6 LOAD cases. MLKL is expressed in neurons, and the its expression levels in the p.Q48X carriers were significantly lower than that in age-matched wild-type controls. The ratio of Aβ42 to Aβ40 significantly increased in MLKL knockdown cells compared to scramble controls. MLKL loss-of-function mutation might contribute to late-onset ApoE ɛ4-negative AD in the Hong Kong Chinese population.

PMID: 29656768 [PubMed - as supplied by publisher]

Malignant cells from pleural fluids in malignant mesothelioma patients reveal novel mutations.

Lung Cancer. 2018 May;119:64-70

Authors: Sneddon S, Dick I, Lee YCG, Musk AWB, Patch AM, Pearson JV, Waddell N, Allcock RJN, Holt RA, Robinson BWS, Creaney J

Abstract
OBJECTIVES: Malignant mesothelioma (MM) is an asbestos related tumour affecting cells of serosal cavities. More than 70% of MM patients develop pleural effusions which contain tumour cells, representing a readily accessible source of malignant cells for genetic analysis. Although common somatic mutations and losses have been identified in solid MM tumours, the characterization of tumour cells within pleural effusions could provide novel insights but is little studied.
MATERIALS AND METHODS: DNA and RNA were extracted from cells from short term cultures of 27 human MM pleural effusion samples. Whole exome and transcriptome sequencing was performed using the Ion Torrent platform. Somatic mutations were identified using VarScan2 and SomaticSniper. Copy number alterations were identified using ExomeCNV in R. Significant copy number alterations were identified across all samples using GISTIC2.0. The association between tumour intrinsic properties and survival was analyzed using the Cox proportional hazards regression model.
RESULTS: We identified BAP1, CDKN2A and NF2 alterations in the cells from MM pleural effusions at a higher frequency than what is typically seen in MM tumours from surgical series. The median mutation rate was 1.09 mutations/Mb. TRAF7 and LATS2 alterations were also identified at a high frequency (66% and 59% respectively). Novel regions of interest were identified, including alterations in FGFR3, and the regions 19p13.3, 8p23.1 and 1p36.32.
CONCLUSION: Short term cultures of tumour cells from MM pleural effusions offer an accessible alternative to surgical tumour biopsies in the study of MM genomics and reveal novel mutations of interest. Pleural effusion tumour cells provide an opportunity for the monitoring of tumour dynamics, treatment response and the clonal evolution of MM tumours.

PMID: 29656754 [PubMed - in process]

Association Between Germline Mutations in BRF1, a Subunit of the RNA Polymerase III Transcription Complex, and Hereditary Colorectal Cancer.

Gastroenterology. 2018 01;154(1):181-194.e20

Authors: Bellido F, Sowada N, Mur P, Lázaro C, Pons T, Valdés-Mas R, Pineda M, Aiza G, Iglesias S, Soto JL, Urioste M, Caldés T, Balbín M, Blay P, Rueda D, Durán M, Valencia A, Moreno V, Brunet J, Blanco I, Navarro M, Calin GA, Borck G, Puente XS, Capellá G, Valle L

Abstract
BACKGROUND & AIMS: Although there is a genetic predisposition to colorectal cancer (CRC), few of the genes that affect risk have been identified. We performed whole-exome sequence analysis of individuals in a high-risk family without mutations in genes previously associated with CRC risk to identify variants associated with inherited CRC.
METHODS: We collected blood samples from 3 relatives with CRC in Spain (65, 62, and 40 years old at diagnosis) and performed whole-exome sequence analyses. Rare missense, truncating or splice-site variants shared by the 3 relatives were selected. We used targeted pooled DNA amplification followed by next generation sequencing to screen for mutations in candidate genes in 547 additional hereditary and/or early-onset CRC cases (502 additional families). We carried out protein-dependent yeast growth assays and transfection studies in the HT29 human CRC cell line to test the effects of the identified variants.
RESULTS: A total of 42 unique or rare (population minor allele frequency below 1%) nonsynonymous genetic variants in 38 genes were shared by all 3 relatives. We selected the BRF1 gene, which encodes an RNA polymerase III transcription initiation factor subunit for further analysis, based on the predicted effect of the identified variant and previous association of BRF1 with cancer. Previously unreported or rare germline variants in BRF1 were identified in 11 of 503 CRC families, a significantly greater proportion than in the control population (34 of 4300). Seven of the identified variants (1 detected in 2 families) affected BRF1 mRNA splicing, protein stability, or expression and/or function.
CONCLUSIONS: In an analysis of families with a history of CRC, we associated germline mutations in BRF1 with predisposition to CRC. We associated deleterious BRF1 variants with 1.4% of familial CRC cases, in individuals without mutations in high-penetrance genes previously associated with CRC. Our findings add additional evidence to the link between defects in genes that regulate ribosome synthesis and risk of CRC.

PMID: 28912018 [PubMed - indexed for MEDLINE]

Systematic analysis of mutation distribution in three dimensional protein structures identifies cancer driver genes.

Sci Rep. 2016 05 26;6:26483

Authors: Fujimoto A, Okada Y, Boroevich KA, Tsunoda T, Taniguchi H, Nakagawa H

Abstract
Protein tertiary structure determines molecular function, interaction, and stability of the protein, therefore distribution of mutation in the tertiary structure can facilitate the identification of new driver genes in cancer. To analyze mutation distribution in protein tertiary structures, we applied a novel three dimensional permutation test to the mutation positions. We analyzed somatic mutation datasets of 21 types of cancers obtained from exome sequencing conducted by the TCGA project. Of the 3,622 genes that had ≥3 mutations in the regions with tertiary structure data, 106 genes showed significant skew in mutation distribution. Known tumor suppressors and oncogenes were significantly enriched in these identified cancer gene sets. Physical distances between mutations in known oncogenes were significantly smaller than those of tumor suppressors. Twenty-three genes were detected in multiple cancers. Candidate genes with significant skew of the 3D mutation distribution included kinases (MAPK1, EPHA5, ERBB3, and ERBB4), an apoptosis related gene (APP), an RNA splicing factor (SF1), a miRNA processing factor (DICER1), an E3 ubiquitin ligase (CUL1) and transcription factors (KLF5 and EEF1B2). Our study suggests that systematic analysis of mutation distribution in the tertiary protein structure can help identify cancer driver genes.

PMID: 27225414 [PubMed - indexed for MEDLINE]

A case report and review of the literature indicate that HMGA2 should be added as a disease gene for Silver-Russell syndrome.

Gene. 2018 Apr 12;:

Authors: Leszinski GS, Warncke K, Hoefele J, Wagner M

Abstract
Patients with Silver-Russell syndrome (SRS), a syndromic growth retardation syndrome, usually harbor a maternal uniparental disomy of chromosome 7 or an epimutation at chromosome 11p15. However, to date the genetic cause remains unknown in around 40% of SRS cases, suggesting genetic heterogeneity and involvement of other genes. We present a 4-year-old female patient with the clinical diagnosis of SRS and negative results in common genetic SRS diagnostics. Whole exome sequencing identified a de novo heterozygous 7.3 kb deletion on chromosome 12q14.3 including exon 1 and 2 of HMGA2. HMGA2 encodes an architectural transcription factor and has already been linked to body size variations in various genome-wide association studies and mouse models. Reviewing the literature, we found additional seven patients with a phenotype of SRS harboring point mutations or structural variants involving HMGA2. We conclude that genetic testing of HMGA2 should be added to routine diagnostics in patients with the suspicion of SRS.

PMID: 29655892 [PubMed - as supplied by publisher]

MARS variant associated with both recessive interstitial lung and liver disease and dominant Charcot-Marie-Tooth disease.

Eur J Med Genet. 2018 Apr 12;:

Authors: Rips J, Meyer-Schuman R, Breuer O, Tsabari R, Shaag A, Revel-Vilk S, Reif S, Elpeleg O, Antonellis A, Harel T

Abstract
Aminoacyl-tRNA synthetases (ARSs) are ubiquitously expressed enzymes responsible for charging tRNA with cognate amino acids during protein translation. Non-canonical functions are increasingly recognized, and include transcription and translation control and extracellular signaling. Monoallelic mutations in genes encoding several ARSs have been identified in axonal Charcot-Marie-Tooth (CMT2) disease, whereas biallelic mutations in ARS loci have been associated with multi-tissue syndromes, variably involving the central nervous system, lung, and liver. We report a male infant of non-consanguineous origin, presenting with successive onset of transfusion-dependent anemia, hypothyroidism, cholestasis, interstitial lung disease, and developmental delay. Whole-exome sequencing (WES) revealed compound heterozygosity for two variants (p.Tyr307Cys and p.Arg618Cys) in MARS, encoding methionyl-tRNA synthetase. Biallelic MARS mutations are associated with interstitial lung and liver disease (ILLD). Interestingly, the p.Arg618Cys variant, inherited from an unaffected father, was previously reported in a family with autosomal dominant late-onset CMT2. Yeast complementation assays confirmed pathogenicity of p.Arg618Cys, yet suggested retained function of p.Tyr307Cys. Our findings underscore the phenotypic variability associated with ARS mutations, and suggest genetic or environmental modifying factors in the onset of monoallelic MARS-associated CMT2.

PMID: 29655802 [PubMed - as supplied by publisher]

Prognostic Impact of Tumor Mutation Burden in Patients with Completely Resected Non-Small Cell Lung Cancer: Brief Report.

J Thorac Oncol. 2018 Apr 11;:

Authors: Owada-Ozaki Y, Muto S, Takagi H, Inoue T, Watanabe Y, Fukuhara M, Yamaura T, Okabe N, Matsumura Y, Hasegawa T, Ohsugi J, Hoshino M, Shio Y, Nanamiya H, Imai JI, Isogai T, Watanabe S, Suzuki H

Abstract
INTRODUCTION: Tumor mutation burden (TMB), is thought to be associated with the amount of neoantigen in the tumor and to have an important role in predicting the effect of immune checkpoint inhibitors. However, the relevance of TMB to prognosis is not yet fully understood. In this study, we investigated the clinical significance of TMB in patients with non-small cell lung cancer (NSCLC) and examined the relationship between TMB and prognosis.
METHODS: We calculated TMB within individual tumors by whole exome sequencing analysis using next-generation sequencing. We included 90 patients with NSCLC who underwent surgery in the Hospital of Fukushima Medical University from 2013 to 2016. No patients received chemotherapy or immunotherapy before surgery. We assessed the correlation between TMB and prognosis.
RESULTS: TMB >62 was associated with worse overall survival (OS) of patients with NSCLC (hazard ratio [HR] = 6.633, P = 0.0003). Multivariate analysis showed poor prognosis with high TMB (HR = 12.31, P = 0.019). In patients with stage I NSCLC, higher TMB was associated with worse prognosis for both OS (HR = 7.582, P = 0.0018) and disease-free survival (HR = 6.07, P = 0.0072).
CONCLUSION: High TMB in NSCLC is a poor prognostic factor. If high TMB is a predictor of the efficacy of immune checkpoint inhibitors, postoperative adjuvant therapy with immune checkpoint inhibitors may contribute to improvement of recurrence and OS.

PMID: 29654927 [PubMed - as supplied by publisher]

Advances in Evaluation of Chronic Diarrhea in Infants.

Gastroenterology. 2018 Apr 11;:

Authors: Thiagarajah JR, Kamin DS, Acra S, Goldsmith JD, Roland JT, Lencer WI, Muise AM, Goldenring JR, Avitzur YA, Martín MG, PediCODE consortium

Abstract
Diarrhea is common in infants (children less than 2 years of age), usually acute, and if chronic, commonly caused by allergies and occasionally by infectious agents. Congenital diarrheas and enteropathies (CODEs) are rare causes of devastating chronic diarrhea in infants. Evaluation of CODEs is a lengthy process and infrequently leads to a clear diagnosis. However, genomic analyses and the development of model systems have increased our understanding of CODE pathogenesis. With these advances, a new diagnostic approach is needed. We propose a revised approach to determine causes of diarrhea in infants, including CODEs, based on stool analysis, histologic features, responses to dietary modifications, and genetic tests. After exclusion of common causes of diarrhea in infants, the evaluation proceeds through analyses of stool characteristics (watery, fatty, or bloody) and histologic features such as the villus to crypt ratio in intestinal biopsies. Infants with CODEs resulting from defects in digestion, absorption, transport of nutrients and electrolytes, or enteroendocrine cell development or function have normal villi to crypt ratios; defects in enterocyte structure or immune-mediated conditions result in an abnormal villus to crypt ratios and morphology. Whole-exome and genome sequencing in the early stages of evaluation can reduce the time required for a definitive diagnosis of CODEs, or lead to identification of new variants associated with these enteropathies. The functional effects of gene mutations can be analyzed in model systems such as enteroids or induced pluripotent stem cells and are facilitated by recent advances in gene editing procedures. Characterization and investigation of new CODE disorders will improve management of patients and advance our understanding of epithelial cells and other cells in the intestinal mucosa.

PMID: 29654747 [PubMed - as supplied by publisher]