Squalene Synthase Deficiency: Clinical, Biochemical, and Molecular Characterization of a Defect in Cholesterol Biosynthesis.

Am J Hum Genet. 2018 Jun 01;:

Authors: Coman D, Vissers LELM, Riley LG, Kwint MP, Hauck R, Koster J, Geuer S, Hopkins S, Hallinan B, Sweetman L, Engelke UFH, Burrow TA, Cardinal J, McGill J, Inwood A, Gurnsey C, Waterham HR, Christodoulou J, Wevers RA, Pitt J

Abstract
Mendelian disorders of cholesterol biosynthesis typically result in multi-system clinical phenotypes, underlining the importance of cholesterol in embryogenesis and development. FDFT1 encodes for an evolutionarily conserved enzyme, squalene synthase (SS, farnesyl-pyrophosphate farnesyl-transferase 1), which catalyzes the first committed step in cholesterol biosynthesis. We report three individuals with profound developmental delay, brain abnormalities, 2-3 syndactyly of the toes, and facial dysmorphisms, resembling Smith-Lemli-Opitz syndrome, the most common cholesterol biogenesis defect. The metabolite profile in plasma and urine suggested that their defect was at the level of squalene synthase. Whole-exome sequencing was used to identify recessive disease-causing variants in FDFT1. Functional characterization of one variant demonstrated a partial splicing defect and altered promoter and/or enhancer activity, reflecting essential mechanisms for regulating cholesterol biosynthesis/uptake in steady state.

PMID: 29909962 [PubMed - as supplied by publisher]

A Novel Strategy Combining Array-CGH, Whole-exome Sequencing and In Utero Electroporation in Rodents to Identify Causative Genes for Brain Malformations.

J Vis Exp. 2017 12 01;(130):

Authors: Conti V, Carabalona A, Pallesi-Pocachard E, Leventer RJ, Schaller F, Parrini E, Deparis AA, Watrin F, Buhler E, Novara F, Lise S, Pagnamenta AT, Kini U, Taylor JC, Zuffardi O, Represa A, Keays DA, Guerrini R, Falace A, Cardoso C

Abstract
Birth defects that involve the cerebral cortex - also known as malformations of cortical development (MCD) - are important causes of intellectual disability and account for 20-40% of drug-resistant epilepsy in childhood. High-resolution brain imaging has facilitated in vivo identification of a large group of MCD phenotypes. Despite the advances in brain imaging, genomic analysis and generation of animal models, a straightforward workflow to systematically prioritize candidate genes and to test functional effects of putative mutations is missing. To overcome this problem, an experimental strategy enabling the identification of novel causative genes for MCD was developed and validated. This strategy is based on identifying candidate genomic regions or genes via array-CGH or whole-exome sequencing and characterizing the effects of their inactivation or of overexpression of specific mutations in developing rodent brains via in utero electroporation. This approach led to the identification of the C6orf70 gene, encoding for a putative vesicular protein, to the pathogenesis of periventricular nodular heterotopia, a MCD caused by defective neuronal migration.

PMID: 29286390 [PubMed - indexed for MEDLINE]

A Patient with a Novel Gene Mutation Leading to Autosomal Dominant Polycystic Kidney Disease.

Clin J Am Soc Nephrol. 2017 10 06;12(10):1695-1698

Authors: Reddy BV, Chapman AB

PMID: 28784653 [PubMed - indexed for MEDLINE]

A novel PTCH1 mutation underlies non-syndromic cleft lip and/or palate in a Han Chinese family.

Oral Dis. 2018 Jun 16;:

Authors: Zhao H, Zhong W, Leng C, Zhang J, Zhang M, Huang W, Zhang Y, Li W, Jia P, Lin J, Maimaitili G, Chen F

Abstract
OBJECTIVES: Cleft lip and/or palate (CL/P) is the most common craniofacial congenital disease, and it has a complex aetiology. This study aimed to identify the causative gene mutation of a Han Chinese family with CL/P.
SUBJECTS AND METHODS: Whole exome sequencing was conducted on the proband and her mother, who exhibited the same phenotype. A Mendelian dominant inheritance model, allele frequency, mutation regions, functional prediction and literature review were used to screen and filter the variants. The candidate was validated by Sanger sequencing. Conservation analysis and homology modelling were conducted.
RESULTS: A heterozygous missense mutation c.1175C>T in the PTCH1 gene predicting p.Ala392Val was identified. This variant has not been reported and was predicted to be deleterious. Sanger sequencing verified the variant and the dominant inheritance model in the family. The missense alteration affects an amino acid that is evolutionarily conserved in the first extracellular loop of the PTCH1 protein. The local structure of the mutant protein was significantly altered according to homology modelling.
CONCLUSIONS: Our findings suggest that c.1175C>T in PTCH1 (NM_000264) may be the causative mutation of this pedigree. Our results add to the evidence that PTCH1 variants play a role in the pathogenesis of orofacial clefts. This article is protected by copyright. All rights reserved.

PMID: 29908092 [PubMed - as supplied by publisher]

Results of next generation sequencing gene panel diagnostics including copy number variation analysis in 810 patients suspected of heritable thoracic aortic disorders.

Hum Mutat. 2018 Jun 16;:

Authors: Overwater E, Marsili L, Baars MJH, Baas AF, van de Beek I, Dulfer E, van Hagen JM, Hilhorst-Hofstee Y, Kempers M, Krapels IP, Menke LA, Verhagen JMA, Yeung KK, Zwijnenburg PJG, Groenink M, van Rijn P, Weiss MM, Voorhoeve E, van Tintelen JP, Houweling AC, Maugeri A

Abstract
Simultaneous analysis of multiple genes using next generation sequencing (NGS) technology has become widely available. Copy number variations (CNVs) in disease-associated genes have emerged as a cause for several hereditary disorders. CNVs are, however, not routinely detected using NGS analysis. The aim of this study was to assess the diagnostic yield and the prevalence of CNVs using our panel of Hereditary Thoracic Aortic Disease (H-TAD) associated genes. 810 patients suspected of H-TAD were analysed by targeted NGS analysis of 21 H-TAD associated genes. In addition, the eXome Hidden Markov Model (XHMM; an algorithm to identify CNVs in targeted NGS data) was used to detect CNVs in these genes. A pathogenic or likely pathogenic variant was found in 66 out of 810 patients (8.1%). Of these 66 pathogenic or likely pathogenic variants, six (9.1%) were CNVs not detectable by routine NGS analysis. These CNVs were four intragenic (multi-)exon deletions in MYLK, TGFB2, SMAD3 and PRKG1 respectively. In addition, a large duplication including NOTCH1 and a large deletion encompassing SCARF2 were detected. As confirmed by additional analyses, both CNVs indicated larger chromosomal abnormalities which could explain the phenotype in both patients. Given the clinical relevance of the identification of a genetic cause, CNV analysis using a method such as XHMM should be incorporated into the clinical diagnostic care for H-TAD patients. This article is protected by copyright. All rights reserved.

PMID: 29907982 [PubMed - as supplied by publisher]

Assessment of the corticospinal fiber integrity in mirror movement disorder.

J Clin Neurosci. 2018 Jun 12;:

Authors: Solmaz B, Özyurt MG, Ata DB, Akçimen F, Shabsog M, Türker KS, Dalçik H, Algin O, Başak AN, Özgür M, Çavdar S

Abstract
Mirror movements are unintended movements occurring on one side of the body that mirror the contralateral voluntary ones. It has been proposed that mirror movements occur due to abnormal decussation of the corticospinal pathways. Using detailed multidisciplinary approach, we aimed to enlighten the detailed mechanism underlying the mirror movements in a case subject who is diagnosed with mirror movements of the hands and we compared the findings with the unaffected control subjects. To evaluate the characteristics of mirror movements, we used several techniques including whole exome sequencing, computed tomography, diffusion tensor imaging and transcranial magnetic stimulation. Computed tomography showed the absence of a spinous process of C5, fusion of the body of C5-C6 vertebrae, hypoplastic dens and platybasia of the posterior cranial fossa. A syrinx cavity was present between levels C3-C4 of the spinal cord. Diffusion tensor imaging of the corticospinal fibers showed disorganization and minimal decussations at the lower medulla oblongata. Transcranial magnetic stimulation showed that motor commands were distributed to the motor neuron pools on the left and right sides of the spinal cord via fast-conducting corticospinal tract fibers. Moreover, a heterozygous missense variation in the deleted in colorectal carcinoma gene has been observed. Developmental absence of the axonal guidance molecules or their receptors may result in abnormalities in the leading of the corticospinal fibers. Clinical evaluations and basic neuroscience techniques, in this case, provide information for this rare disease and contribute to our understanding of the normal physiology of bimanual coordination.

PMID: 29907388 [PubMed - as supplied by publisher]

PROMIDISα: a TCRα signature associated with immunodeficiencies caused by V(D)J recombination defects.

J Allergy Clin Immunol. 2018 Jun 12;:

Authors: Berland A, Rosain J, Kaltenbach S, Allain V, Mahlaoui N, Melki I, Fievet A, Dubois d'Enghien C, Ouachée-Chardin M, Perrin L, Auger N, Cipe FE, Finocchi A, Dogu F, Suarez F, Moshous D, Leblanc T, Belot A, Fieschi C, Boutboul D, Malphettes M, Galicier L, Oksenhendler E, Blanche S, Fischer A, Revy P, Stoppa-Lyonnet D, Picard C, de Villartay JP

Abstract
- BACKGROUND: V(D)J recombination ensures the diversity of the adaptive immune system. While its complete defect causes Severe Combined Immunodeficiency (T-B-SCID), its suboptimal activity, is associated with a broad spectrum of immune manifestations such as late onset combined immunodeficiency and autoimmunity. The earliest molecular diagnosis of these patients is required to adopt the best therapy strategy, in particular when it involves myelo-ablative conditioning regimen for hematopoietic stem cell transplantation (HSCT).
- OBJECTIVE: We aimed at developing biomarkers based on the analysis of TCRα repertoire to assist in the diagnosis of primary immunodeficient patients (PID) with V(D)J recombination and DNA repair deficiencies.
- METHODS: We used flow cytometry (FACS) analysis to quantify TCR-Vα7.2 expressing T lymphocytes in peripheral blood and developed PROMIDISα, a multiplex RT-PCR/NGS assay, to evaluate a subset of the TCRα repertoire in T lymphocytes.
- RESULTS: The combined FACS and PROMIDISα analyses revealed specific signatures in patients with V(D)J recombination defective PIDs or Ataxia telangiectasia/Nijmegen breakage syndromes (AT/NBS).
- CONCLUSION: Analysis of the TCRα repertoire is particularly appropriate, in a prospective way, to identify patients with partial immune defects caused by suboptimal V(D)J recombination activity and/or DNA repair defect. It also constitutes a valuable tool for the retrospective in vivo functional validation of variants identified through exome or panel sequencing. Its broader implementation may be of interest to assist early diagnosis of patients presenting with hypomorphic DNA repair defects inclined to develop acute toxicity during pre-HSCT conditioning.

PMID: 29906526 [PubMed - as supplied by publisher]

From exome analysis in idiopathic azoospermia to the identification of a high-risk subgroup for occult Fanconi anemia.

Genet Med. 2018 Jun 14;:

Authors: Krausz C, Riera-Escamilla A, Chianese C, Moreno-Mendoza D, Ars E, Rajmil O, Pujol R, Bogliolo M, Blanco I, Rodríguez I, Badell I, Ruiz-Castañé E, Surrallés J

Abstract
PURPOSE: In about 10% of patients affected by Fanconi anemia (FA) the diagnosis is delayed until adulthood, and the presenting symptom in these "occult" FA cases is often a solid cancer and cancer treatment-related toxicity. Highly predictive clinical parameter(s) for diagnosing such an adult-onset cases are missing.
METHODS: (1) Exome sequencing (ES), (2) Sanger sequencing of FANCA, (3) diepoxybutane (DEB)-induced chromosome breakage test.
RESULTS: ES identified a pathogenic homozygous FANCA variant in a patient affected by Sertoli cell-only syndrome (SCOS) and in his azoospermic brother. Although they had no overt anemia, chromosomal breakage test revealed a reverse somatic mosaicism in the former and a typical FA picture in the latter. In 27 selected SCOS cases, 1 additional patient showing compound heterozygous pathogenic FANCA variants was identified with positive chromosomal breakage test.
CONCLUSION: We report an extraordinarily high frequency of FA in a specific subgroup of azoospermic patients (7.1%). The screening for FANCA pathogenic variants in such patients has the potential to identify undiagnosed FA before the appearance of other severe clinical manifestations of the disease. The definition of this high-risk group for "occult" FA, based on specific testis phenotype with mild/borderline hematological alterations, is of unforeseen clinical relevance.

PMID: 29904161 [PubMed - as supplied by publisher]

ATP13A2 novel mutations causing a rare form of juvenile-onset Parkinson disease.

Brain Dev. 2018 Jun 11;:

Authors: Suleiman J, Hamwi N, El-Hattab AW

Abstract
Parkinson disease is a common neurodegenerative disease that typically starts around the age of 60 years; however, juvenile-onset disease can occur rarely. Although Parkinson disease is typically sporadic; in rare occasions, it can be caused by a single gene defect that is inherited in an autosomal dominant, autosomal recessive, or X-linked manner. Herein, we describe a 10-year-old child who had juvenile-onset parkinsonism with rigidity, bradykinesia, dystonia, gait disturbance, and cognitive impairment. Whole exome sequencing showed compound heterozygosity for two previously unreported novel mutations in ATP13A2 (PARK9): a paternally inherited c.1321A>T (p.I441F) and a maternally inherited c.3205G>A (p.A1069T). ATP13A2 mutations are rare cause of autosomal recessive juvenile-onset Parkinson disease. Family co-segregation study and the clinical phenotype support that p.I441F and p.A1069T are indeed disease-causing mutations.

PMID: 29903538 [PubMed - as supplied by publisher]

Genetic epidemiology of neural tube defects.

J Pediatr Rehabil Med. 2017 Dec 11;10(3-4):189-194

Authors: Lupo PJ, Agopian AJ, Castillo H, Castillo J, Clayton GH, Dosa NP, Hopson B, Joseph DB, Rocque BG, Walker WO, Wiener JS, Mitchell LE

Abstract
It has been estimated that 60-70% of neural tube defects (NTDs) have a genetic component, but few causative genes have been identified. The lack of information on genes associated with non-syndromic NTDs in humans is especially notable as the "genomic revolution" has led to new tools (e.g., genome-wide genotyping arrays, next-generation sequencing) that are helping to elucidate the full spectrum of genetic variation (from common to rare) contributing to complex traits, including structural birth defects. However, the application of modern genomic approaches to the study of NTDs has lagged behind that of some other common structural birth defects. This may be due to the difficulty of assembling large study cohorts for anencephaly or spina bifida. The purpose of this review is to outline the evolution of genetic studies of NTDs, from studies of familial aggregation to candidate gene and genome-wide association studies, through whole-exome and whole-genome sequencing. Strategies for addressing gaps in NTD genetic research are also explored.

PMID: 29125517 [PubMed - indexed for MEDLINE]

Genetic predisposition in children with cancer - affected families' acceptance of Trio-WES.

Eur J Pediatr. 2018 Jan;177(1):53-60

Authors: Brozou T, Taeubner J, Velleuer E, Dugas M, Wieczorek D, Borkhardt A, Kuhlen M

Abstract
A considerable percentage of childhood cancers are due to cancer predisposition syndromes (CPS). The ratio of CPSs caused by inherited versus de novo germline mutations and the risk of recurrence in other children are unknown. We initiated a prospective study performing whole-exome sequencing (WES) of parent-child trios in children newly diagnosed with cancer. We initially aimed to determine the interest in and acceptance of trio WES among affected families and to systematically collect demographic, medical, and family history data to analyze whether these point to an underlying CPS. Between January 2015 and December 2016, 83 (88.3%) of 94 families participated; only 11 (11.7%) refused to participate. Five (6.0%) children presented with congenital malignancies and three (3.6%) with tumors with a high likelihood of an underlying CPS. Two (2.5%) families showed malignancies in family members < 18 years, 11 (13.8%) showed relatives < 45 years with cancer, 37 (46.3%) had a positive cancer history, and 14 (17.5%) families had > 1 relative with cancer.
CONCLUSIONS: Genetic testing in pediatric oncology is of great interest to the families, and the vast majority opts for investigation into potentially underlying CPSs. Trio sequencing provides unique insights into CPS in pediatric cancers and is increasingly becoming a common approach in modern oncology, and thus, trio sequencing needs also to be integrated routinely into the practice of pediatric oncology. What is Known: • A considerable percentage of childhood cancers are due to cancer predisposition syndromes (CPS). What is New: • Knowing about an underlying CPS and, thus, the risk of recurrence in other children is of great interest to affected families.

PMID: 28929227 [PubMed - indexed for MEDLINE]

A novel deletion downstream of the PAX6 gene identified in a Chinese family with congenital aniridia.

Ophthalmic Genet. 2018 Jun 14;:1-9

Authors: Liu X, Wu Y, Miao Z, Zhang H, Gong B, Zhu X, Huang L, Shi Y, Hao F, Ma S, Lin H, Wang L, Yang Z

Abstract
PURPOSE: Congenital aniridia, a severe bilateral panocular visual disorder, is an autosomal dominantly inherited eye anomaly. Mutations in the paired box 6 gene (PAX6) have been shown to be responsible for congenital aniridia in most patients. The purpose of the present study was to report clinical features of a Chinese family with congenital aniridia and to screen novel genetic mutations for congenital aniridia.
METHODS: All members of a three-generation family underwent comprehensive ophthalmic examination, and 8 of its 25 members were diagnosed with congenital aniridia. The proband was analyzed by exome sequencing and whole genome sequencing, and linkage analysis was performed for the family. The mutation was confirmed by direct DNA sequencing.
RESULTS: Using Illumina's Human Linkage-12 beadchip microarray (including 6090 SNPs) whole genome scan, the LOD score value showed that the interval on chromosome 11 between rs1389423 to rs910090 exhibited a strong linkage. A novel heterozygous 469 kb deletion mutation within the downstream region of PAX6 (chr11:31189937-31659379) was identified in all affected family members, but not in unaffected family members or 2000 ethnically matched controls.
CONCLUSION: A novel deletion mutation was identified within the PAX6 downstream region that results in congenital aniridia.

PMID: 29902091 [PubMed - as supplied by publisher]

Novel intra-genic large deletions of CTNNB1 gene identified in WT desmoid-type fibromatosis.

Genes Chromosomes Cancer. 2018 Jun 14;:

Authors: Colombo C, Urbini M, Astolfi A, Collini P, Indio V, Belfiore A, Paielli N, Perrone F, Tarantino G, Palassini E, Fiore M, Pession A, Stacchiotti S, Pantaleo MA, Gronchi A

Abstract
A wait and see approach for desmoid tumors (DT) has become part of the routine treatment strategy. However, predictive factors to select the risk of progressive disease are still lacking. A translational project was run in order to identify genomic signatures in patients enrolled within an Italian prospective observational study. Among 12 DT patients (ten CTNNB1-mutated and two WT) enrolled from our Institution only two patients (17%) showed a progressive disease. Tumor biopsies were collected for whole exome sequencing. Overall, DT exhibited low somatic sequence mutation rate and no additional recurrent mutation was found. In the two WT cases, two novel alterations were detected: a complex deletion of APC and a pathogenic mutation of LAMTOR2. Focusing on WT DT subtype, deep sequencing of CTNNB1, APC and LAMTOR2 was conducted on a retrospective series of 11 WT DT using a targeted approach. No other mutation of LAMTOR2 was detected, while APC was mutated in two cases. Low-frequency (mean reads of 16%) CTNNB1 mutations were discovered in five samples (45%) and two novel intra-genic deletions in CTNNB1 were detected in two cases. Both deletions and low frequency mutations of CTNNB1 were highly expressed. In conclusion, a minority of DT is WT for either CTNNB1, APC or any other gene involved in the WNT pathway. In this subgroup novel and hard to be detected molecular alterations in APC and CTNNB1 were discovered, contributing to explain a portion of the allegedly WT DT cases. This article is protected by copyright. All rights reserved.

PMID: 29901254 [PubMed - as supplied by publisher]

Targeted resequencing of phosphorus metabolism‑related genes in 86 patients with hypophosphatemic rickets/osteomalacia.

Int J Mol Med. 2018 Jun 13;:

Authors: Gu J, Wang C, Zhang H, Yue H, Hu W, He J, Fu W, Zhang Z

Abstract
Hypophosphatemic rickets/osteomalacia is characterized by defective renal phosphate reabsorption and abnormal bone mineralization. Hypophosphatemic rickets/osteomalacia consists of inherited and acquired forms, many of which have unknown aetiology. In the present study, next‑generation sequencing‑based resequencing was used on samples from Chinese subjects with hypophosphatemic rickets/osteomalacia, aiming to detect the spectrum of pathogenic genes in these patients. A total of 86 hypophosphatemic rickets/osteomalacia patients (ranging from 3 to 70 years old) were recruited. Patients with tumour‑induced osteomalacia (TIO), renal tubular acidosis, renal osteodystrophy, and adefovir‑induced Fanconi syndrome were excluded. Targeted massively parallel resequencing of 196 candidate genes for hypophosphatemic rickets/osteomalacia was performed in the 86 affected unrelated individuals (cases) and in 100 unrelated healthy controls to identify new genes and mutations in known genes that cause hypophosphatemic rickets/osteomalacia. The results identified seven phosphate‑regulating gene with homologies to endopeptidases on the X chromosome (PHEX) mutations (of which two were novel) and one novel dentin matrix protein 1 (DMP1) mutation in eight patients. Following targeted exome sequencing data analysis, 14 candidate disease‑related gene loci were selected, two of which were of most concern regarding disease severity. Further validation of the present results is warranted, with additional sequencing projects and functional tests. To our knowledge, the present study is the largest cohort of cases with hypophosphatemic rickets/osteomalacia to undergo targeted resequencing. The diagnosis and understanding of the molecular aetiologies of these disorders will be improved by this fast and efficient approach.

PMID: 29901142 [PubMed - as supplied by publisher]

Novel HSPG2 mutations causing Schwartz‑Jampel syndrome type 1 in a Chinese family: A case report.

Mol Med Rep. 2018 Jun 06;:

Authors: Yan W, Dai J, Shi D, Xu X, Han X, Xu Z, Chen D, Teng H, Jiang Q

Abstract
Schwartz-Jampel syndrome type 1 (SJS1) is a rare autosomal recessive disease caused by mutations in the gene heparan sulfate proteoglycan 2 (HSPG2; also known as basement membrane‑specific heparin sulfate). In the present study, a 10‑year‑old female SJS1 proband from a Chinese family, who was diagnosed by X‑ray and physical examination, was recruited. The key clinical features of the patient with SJS1 included short stature, joint contractures, pigeon breast, and myotonia that led to progressive stiffness of the face and limbs; barely discernible kyphosis was also noted. Genetic testing using whole exome sequencing and Sanger sequencing was performed for the proband and family members. A total of 2 novel mutations (c.8788G>A; p.Glu2930Lys and c.11671+5G>A) in the HSPG2 gene were identified in the proband. The family members harboring 1 heterozygous mutation in HSPG2 did not exhibit any skeletal abnormalities. The results of the present study suggested that the compound heterozygous mutations in HSPG2 may be responsible the induction of SJS1, and demonstrated the genotype‑phenotype associations between mutations in the HSPG2 gene and clinical characteristics of SJS1.

PMID: 29901129 [PubMed - as supplied by publisher]

Developmental epileptic encephalopathy with hypomyelination and brain atrophy associated with PTPN23 variants affecting the assembly of UsnRNPs.

Eur J Hum Genet. 2018 Jun 13;:

Authors: Smigiel R, Landsberg G, Schilling M, Rydzanicz M, Pollak A, Walczak A, Stodolak A, Stawinski P, Mierzewska H, Sasiadek MM, Gruss OJ, Ploski R

Abstract
PTPN23 encodes a ubiquitously expressed non-receptor type, catalytically inactive protein-tyrosine phosphatase found in all cells including neurons. Recently, we have identified PTPN23 in a cellular screen for the systematic identification of novel regulators of survival motor neuron (SMN) function in the assembly of splicing factors (Uridine-rich small nuclear ribonucleoproteins, UsnRNPs). Based on three families, recessive PTPN23 variants have been associated with human disease tentatively, without functional studies. Here, we describe a pediatric proband with severe developmental delay, epilepsy, cortical blindness, hypomyelination and brain atrophy on MRI. Whole exome sequencing and family study showed two novel PTPN23 variants, c.1902C>G (p.(Asn634Lys)) and c.2974delC (p.(Leu992Tyrfs*168)), in compound heterozygous state, which are predicted in silico to be damaging. When studying patient's fibroblasts we found similar expression of SMN but a dramatic reduction of cells displaying SMN accumulation in Cajal bodies (CB). SMN strongly accumulated in CB in more than 50% of unrelated control cell fibroblasts as well as in fibroblasts from the parent carrying only the c.2974delC (p.(Leu992Tyrfs*168)) variant (predicted to cause loss-of-function). In contrast, only 22% of cells showed respective SMN accumulations in patient fibroblasts (p = 1.9-2.5 × 10-7) while showing a higher level of nucleoplasmic SMN. Furthermore, the remaining accumulations in patient cells displayed weaker SMN signals than control or heterozygous wt/c.2974delC (p.(Leu992Tyrfs*168)) fibroblasts. Our report provides the first description of the clinical phenotype of recessive PTPN23 variants with pathogenicity substantiated by a functional study.

PMID: 29899372 [PubMed - as supplied by publisher]

Calculating the statistical significance of rare variants causal for Mendelian and complex disorders.

BMC Med Genomics. 2018 Jun 13;11(1):53

Authors: Rao AR, Nelson SF

Abstract
BACKGROUND: With the expanding use of next-gen sequencing (NGS) to diagnose the thousands of rare Mendelian genetic diseases, it is critical to be able to interpret individual DNA variation. To calculate the significance of finding a rare protein-altering variant in a given gene, one must know the frequency of seeing a variant in the general population that is at least as damaging as the variant in question.
METHODS: We developed a general method to better interpret the likelihood that a rare variant is disease causing if observed in a given gene or genic region mapping to a described protein domain, using genome-wide information from a large control sample. Based on data from 2504 individuals in the 1000 Genomes Project dataset, we calculated the number of individuals who have a rare variant in a given gene for numerous filtering threshold scenarios, which may be used for calculating the significance of an observed rare variant being causal for disease. Additionally, we calculated mutational burden data on the number of individuals with rare variants in genic regions mapping to protein domains.
RESULTS: We describe methods to use the mutational burden data for calculating the significance of observing rare variants in a given proportion of sequenced individuals. We present SORVA, an implementation of these methods as a web tool, and we demonstrate application to 20 relevant but diverse next-gen sequencing studies. Specifically, we calculate the statistical significance of findings involving multi-family studies with rare Mendelian disease and a large-scale study of a complex disorder, autism spectrum disorder. If we use the frequency counts to rank genes based on intolerance for variation, the ranking correlates well with pLI scores derived from the Exome Aggregation Consortium (ExAC) dataset (ρ = 0.515), with the benefit that the scores are directly interpretable.
CONCLUSIONS: We have presented a strategy that is useful for vetting candidate genes from NGS studies and allows researchers to calculate the significance of seeing a variant in a given gene or protein domain. This approach is an important step towards developing a quantitative, statistics-based approach for presenting clinical findings.

PMID: 29898714 [PubMed - in process]

Novel Aberrations Uncovered in Barrett's Esophagus and Esophageal Adenocarcinoma Using Whole Transcriptome Sequencing.

Mol Cancer Res. 2017 Nov;15(11):1558-1569

Authors: Maag JLV, Fisher OM, Levert-Mignon A, Kaczorowski DC, Thomas ML, Hussey DJ, Watson DI, Wettstein A, Bobryshev YV, Edwards M, Dinger ME, Lord RV

Abstract
Esophageal adenocarcinoma (EAC) has one of the fastest increases in incidence of any cancer, along with poor five-year survival rates. Barrett's esophagus (BE) is the main risk factor for EAC; however, the mechanisms driving EAC development remain poorly understood. Here, transcriptomic profiling was performed using RNA-sequencing (RNA-seq) on premalignant and malignant Barrett's tissues to better understand this disease. Machine-learning and network analysis methods were applied to discover novel driver genes for EAC development. Identified gene expression signatures for the distinction of EAC from BE were validated in separate datasets. An extensive analysis of the noncoding RNA (ncRNA) landscape was performed to determine the involvement of novel transcriptomic elements in Barrett's disease and EAC. Finally, transcriptomic mutational investigation of genes that are recurrently mutated in EAC was performed. Through these approaches, novel driver genes were discovered for EAC, which involved key cell cycle and DNA repair genes, such as BRCA1 and PRKDC. A novel 4-gene signature (CTSL, COL17A1, KLF4, and E2F3) was identified, externally validated, and shown to provide excellent distinction of EAC from BE. Furthermore, expression changes were observed in 685 long noncoding RNAs (lncRNA) and a systematic dysregulation of repeat elements across different stages of Barrett's disease, with wide-ranging downregulation of Alu elements in EAC. Mutational investigation revealed distinct pathways activated between EAC tissues with or without TP53 mutations compared with Barrett's disease. In summary, transcriptome sequencing revealed altered expression of numerous novel elements, processes, and networks in EAC and premalignant BE.Implications: This study identified opportunities to improve early detection and treatment of patients with BE and esophageal adenocarcinoma. Mol Cancer Res; 15(11); 1558-69. ©2017 AACR.

PMID: 28751461 [PubMed - indexed for MEDLINE]

Associations of MAP2K3 Gene Variants With Superior Memory in SuperAgers.

Front Aging Neurosci. 2018;10:155

Authors: Huentelman MJ, Piras IS, Siniard AL, De Both MD, Richholt RF, Balak CD, Jamshidi P, Bigio EH, Weintraub S, Loyer ET, Mesulam MM, Geula C, Rogalski EJ

Abstract
Introduction: SuperAgers are adults age 80+ with episodic memory performance that is at least as good as that of average middle-aged adults. Understanding the biological determinants of SuperAging may have relevance to preventing age-related cognitive decline and dementia. This study aimed to identify associations between genetic variations and the SuperAging phenotype using Whole Exome Sequencing (WES). Methods: Sequence Kernel Association Combined (SKAT-C) test was conducted at the gene level including both rare and common variants in 56 SuperAgers and 22 cognitively-average controls from the Alzheimer's disease Neuroimaging Initiative (ADNI). Results: The SuperAging phenotype was associated with variants in the Mitogen-Activated Protein Kinase Kinase 3 (MAP2K3) gene. Three single nucleotide polymorphisms (SNPs) contributed to the significance (rs2363221 [intron 1], rs2230435 [exon 5], rs736103 [intron 7]). Conclusions: MAP2K3 resides in a biological pathway linked to memory. It is in a signaling cascade associated with beta-amyloid mediated apoptosis and has enriched expression in microglia. This preliminary work suggests MAP2K3 may represent a novel therapeutic target for age-related memory decline and perhaps Alzheimer's disease (AD).

PMID: 29896098 [PubMed]

Genome-wide sequencing in acutely ill infants: genomic medicine's critical application?

Genet Med. 2018 Jun 12;:

Authors: Friedman JM, Bombard Y, Cornel MC, Fernandez CV, Junker AK, Plon SE, Stark Z, Knoppers BM, Paediatric Task Team of the Global Alliance for Genomics and Health Regulatory and Ethics Work Stream

Abstract
Diagnostic genome-wide sequencing (exome or genome sequencing and data analysis for high-penetrance disease-causing variants) in acutely ill infants appears to be clinically useful, but the value of this diagnostic test should be rigorously demonstrated before it is accepted as a standard of care. This white paper was developed by the Paediatric Task Team of the Global Alliance for Genomics and Health's Regulatory and Ethics Work Stream to address the question of how we can determine the clinical value of genome-wide sequencing in infants in an intensive care setting. After reviewing available clinical and ethics literature on this question, we conclude that evaluating diagnostic genome-wide sequencing as a comprehensive scan for major genetic disease (rather than as a large panel of single-gene tests) provides a practical approach to assessing its clinical value in acutely ill infants. Comparing the clinical value of diagnostic genome-wide sequencing to chromosomal microarray analysis, the current evidence-based standard of care, per case of serious genetic disease diagnosed provides a practical means of assessing clinical value. Scientifically rigorous studies of this kind are needed to determine if clinical genome-wide sequencing should be established as a standard of care supported by healthcare systems and insurers for diagnosis of genetic disease in seriously ill newborn infants.

PMID: 29895853 [PubMed - as supplied by publisher]