[From a Ph.D. Thesis: Understanding the Past, Predicting the Future].

Yakugaku Zasshi. 2018;138(2):211-219

Authors: Watanabe K

Abstract
　Posey et al. have reported multiple molecular diagnoses in 4.5% of cases (101/2076) in which whole-exome sequencing was informative. Distinct disease phenotypes affect different organ systems, whereas overlapping disease phenotypes are more likely to be caused by two genes encoding proteins that interact within the same pathway. My research projects at the Niigata University of Pharmacy have investigated underlying mechanisms involved in human disease, including fatty acid metabolism, diabetic cardiomyopathy, atopic dermatitis, colitis, hepatitis, etc. Three students from abroad graduated this year from the Department of Clinical Pharmacology, Niigata University of Pharmacy and Applied Life Sciences. These students reported on treatments for heart disease, non-alcoholic steatohepatitis and atopic dermatitis, as well as the underlying mechanisms involved in each. The titles of these reports are "Study of the role of cardiac 14-3-3η protein in cardiac inflammation and adverse cardiac remodeling during heart failure in mice", "Non-alcoholic steatohepatitis: onset of mechanisms under diabetic background and treatment strategies" and "The role of HMGB1 and its cascade signaling pathway in atopic dermatitis". It can be concluded from these three theses that oxidative stress and inflammation are among the principal mechanisms underlying these diseases.

PMID: 29386434 [PubMed - in process]

Unraveling genetic predisposition to familial or early onset gastric cancer using germline whole-exome sequencing.

Eur J Hum Genet. 2017 Nov;25(11):1246-1252

Authors: Vogelaar IP, van der Post RS, van Krieken JHJ, Spruijt L, van Zelst-Stams WA, Kets CM, Lubinski J, Jakubowska A, Teodorczyk U, Aalfs CM, van Hest LP, Pinheiro H, Oliveira C, Jhangiani SN, Muzny DM, Gibbs RA, Lupski JR, de Ligt J, Vissers LELM, Hoischen A, Gilissen C, van de Vorst M, Goeman JJ, Schackert HK, Ranzani GN, Molinaro V, Gómez García EB, Hes FJ, Holinski-Feder E, Genuardi M, Ausems MGEM, Sijmons RH, Wagner A, van der Kolk LE, Bjørnevoll I, Høberg-Vetti H, van Kessel AG, Kuiper RP, Ligtenberg MJL, Hoogerbrugge N

Abstract
Recognition of individuals with a genetic predisposition to gastric cancer (GC) enables preventive measures. However, the underlying cause of genetic susceptibility to gastric cancer remains largely unexplained. We performed germline whole-exome sequencing on leukocyte DNA of 54 patients from 53 families with genetically unexplained diffuse-type and intestinal-type GC to identify novel GC-predisposing candidate genes. As young age at diagnosis and familial clustering are hallmarks of genetic tumor susceptibility, we selected patients that were diagnosed below the age of 35, patients from families with two cases of GC at or below age 60 and patients from families with three GC cases at or below age 70. All included individuals were tested negative for germline CDH1 mutations before or during the study. Variants that were possibly deleterious according to in silico predictions were filtered using several independent approaches that were based on gene function and gene mutation burden in controls. Despite a rigorous search, no obvious candidate GC predisposition genes were identified. This negative result stresses the importance of future research studies in large, homogeneous cohorts.

PMID: 28875981 [PubMed - indexed for MEDLINE]

NDUFAF4 variants are associated with Leigh syndrome and cause a specific mitochondrial complex I assembly defect.

Eur J Hum Genet. 2017 Nov;25(11):1273-1277

Authors: Baertling F, Sánchez-Caballero L, van den Brand MAM, Wintjes LT, Brink M, van den Brandt FA, Wilson C, Rodenburg RJT, Nijtmans LGJ

Abstract
Mitochondrial respiratory chain complex I consists of 44 different subunits and can be subgrouped into three functional modules: the Q-, the P- and the N-module. NDUFAF4 (C6ORF66) is an assembly factor of complex I that associates with assembly intermediates of the Q-module. Via exome sequencing, we identified a homozygous missense variant in a complex I-deficient patient with Leigh syndrome. Supercomplex analysis in patient fibroblasts revealed specifically altered stoichiometry. Detailed assembly analysis of complex I, indicative of all of its assembly routes, showed an accumulation of parts of the P- and the N-module but not the Q-module. Lentiviral complementation of patient fibroblasts with wild-type NDUFAF4 rescued complex I deficiency and the assembly defect, confirming the causal role of the variant. Our report on the second family affected by an NDUFAF4 variant further characterizes the phenotypic spectrum and sheds light into the role of NDUFAF4 in mitochondrial complex I biogenesis.

PMID: 28853723 [PubMed - indexed for MEDLINE]

Rare Variants in Tissue Inhibitor of Metalloproteinase 2 as a Risk Factor for Schizophrenia: Evidence From Familial and Cohort Analysis.

Schizophr Bull. 2018 Jan 29;:

Authors: John J, Sharma A, Kukshal P, Bhatia T, Nimgaonkar VL, Deshpande SN, Thelma BK

Abstract
Candidate gene and genome-wide association study based common risk variant identification is being complemented by whole exome sequencing (WES)/whole genome sequencing based rare variant discovery in elucidation of genetic landscape of schizophrenia (SZ), a common neuropsychiatric disorder. WES findings of de novo mutations in case-parent trios have further implied genetic etiology, but do not explain the high genetic risk in general populations. Conversely, WES in multiplex families may be an insightful strategy for the identification of highly penetrant rare variants in SZ and possibly enhance our understanding of disease biology. In this study, we analyzed a 5-generation Indian family with multiple members affected with SZ by WES. We identified a rare heterozygous missense variant (NM_003255: c.506C>T; p.Pro169Leu; MAF = 0.0001) in Tissue Inhibitor of Metalloproteinase 2 (TIMP2, 17q25.3) segregating with all 6 affected individuals but not with unaffected members. Linkage analysis indicated a maximum logarithm of the odds score of 1.8, θ = 0 at this locus. The variant was predicted to be damaging by various in silico tools and also disrupt the structural integrity by molecular dynamics simulations. WES based screening of an independent SZ cohort (n = 370) identified 4 additional rare missense variants (p.Leu20Met, p.Ala26Ser, p.Lys48Arg and p. Ile217Leu) and a splice variant rs540397728 (NM_003255:c.232-5T>C), also predicted to be damaging, increasing the likelihood of contribution of this gene to SZ risk. Extensive biochemical and knockout mouse studies suggesting involvement of TIMP2 in neurodevelopmental and behavioral deficits, together with genetic evidence for TIMP2 conferring SZ risk from this study may have possible implications for new therapeutics.

PMID: 29385606 [PubMed - as supplied by publisher]

Tumor exome sequencing and copy number alterations reveal potential predictors of intrinsic resistance to multi-targeted tyrosine kinase inhibitors.

Oncotarget. 2017 Dec 29;8(70):115114-115127

Authors: Gillis NK, Rotroff DM, Mesa TE, Yao J, Chen Z, Carulli MA, Yoder SJ, Walko CM, Teer JK, McLeod HL

Abstract
Multi-targeted tyrosine kinase inhibitors (TKIs) have broad efficacy and similar FDA-approved indications, suggesting shared molecular drug targets across cancer types. Irrespective of tumor type, 20-30% of patients treated with multi-targeted TKIs demonstrate intrinsic resistance, with progressive disease as a best response. We conducted a retrospective cohort study to identify tumor (somatic) point mutations, insertion/deletions, and copy number alterations (CNA) associated with intrinsic resistance to multi-targeted TKIs. Using a candidate gene approach (n=243), tumor next-generation sequencing and CNA data was associated with resistant and non-resistant outcomes. Resistant individuals (n=11) more commonly harbored somatic point mutations in NTRK1, KDR, TGFBR2, and PTPN11 and CNA in CDK4, CDKN2B, and ERBB2 compared to non-resistant (n=26, p<0.01). Using a random forest classification model for variable reduction and a decision tree classification model, we were able to differentiate intrinsically resistant from non-resistant patients. CNA in CDK4 and CDKN2B were the most important analytical features, implicating the cyclin D pathway as a potentially important factor in resistance to multi-targeted TKIs. Replication of these results in a larger, independent patient cohort has potential to inform personalized prescribing of these widely utilized agents.

PMID: 29383146 [PubMed]

Myopia in Chinese families shows linkage to 10q26.13.

Mol Vis. 2018;24:29-42

Authors: Musolf AM, Simpson CL, Long KA, Moiz BA, Lewis DD, Middlebrooks CD, Portas L, Murgia F, Ciner EB, Bailey-Wilson JE, Stambolian D

Abstract
Purpose: To determine genetic linkage between myopia and Han Chinese patients with a family history of the disease.
Methods: One hundred seventy-six Han Chinese patients from 34 extended families were given eye examinations, and mean spherical equivalent (MSE) in diopters (D) was calculated by adding the spherical component of the refraction to one-half the cylindrical component and taking the average of both eyes. The MSE was converted to a binary phenotype, where all patients with an MSE of -1.00 D or less were coded as affected. Unaffected individuals had an MSE greater than 0.00 D (ages 21 years and up), +1.50 (ages 11-20), or +2.00 D (ages 6-10 years). Individuals between the given upper threshold and -1.00 were coded as unknown. Patients were genotyped on an exome chip. Three types of linkage analyses were performed: single-variant two-point, multipoint, and collapsed haplotype pattern (CHP) variant two-point.
Results: The CHP variant two-point results identified a significant peak (heterogeneity logarithm of the odds [HLOD] = 3.73) at 10q26.13 in TACC2. The single-variant two-point and multipoint analyses showed highly suggestive linkage to the same region. The single-variant two-point results identified 25 suggestive variants at HTRA1, also at 10q26.13.
Conclusions: We report a significant genetic linkage between myopia and Han Chinese patients at 10q26.13. 10q26.13 contains several good candidate genes, such as TACC2 and the known age-related macular degeneration gene HTRA1. Targeted sequencing of the region is planned to identify the causal variant(s).

PMID: 29383007 [PubMed - in process]

Case report: an unusual case of Brugada syndrome combined with a ventricular septal defect: A case report.

Medicine (Baltimore). 2017 Nov;96(47):e8695

Authors: Liu X, Zheng J, Fan Z, Rao L

Abstract
RATIONALE: Brugada syndrome (BrS) is a cardiac ion channel disease that is caused by an autosomal dominant genetic abnormality. A ventricular septal defect is a common congenital heart disease, in which genetic defects play a significant role.
PATIENT CONCERNS: We report an extremely rare case of a 42-year-old male with congenital heart disease, who suffered recurrent syncope and gastrointestinal bleeding. His electrocardiogram showed an unusual right bundle branch block-like pattern and ST-segment elevation in leads V1-V3.
DIAGNOSES: The patient was eventually diagnosed with Brugada Syndrome Combined with a Ventricular Septal Defect.
INTERVENTIONS: The patient was treated with ICD implants.
OUTCOMES: We extracted his blood and performed whole exome sequencing. Whole exome sequencing revealed mutations in genes, which encode ion channels and proteins important for embryonic heart development. However, a novel mutation in the SCN5A gene was also found.
LESSONS: To our knowledge, this is the first genetically proven case of BrS combined with a ventricular septal defect.

PMID: 29381953 [PubMed - in process]

Clinical and genetic features of Charcot-Marie-Tooth disease 2F and hereditary motor neuropathy 2B in Japan.

J Peripher Nerv Syst. 2018 Jan 30;:

Authors: Tanabe H, Higuchi Y, Yuan JH, Hashiguchi A, Yoshimura A, Ishihara S, Nozuma S, Okamoto Y, Matsuura E, Ishiura H, Mitsui J, Takashima R, Kokubun N, Maeda K, Asano Y, Sunami Y, Kono Y, Ishigaki Y, Yanamoto S, Fukae J, Kida H, Morita M, Tsuji S, Takashima H

Abstract
Mutations in small heat shock protein beta-1 (HspB1) have been linked to Charcot-Marie-Tooth (CMT) disease type 2F and distal hereditary motor neuropathy type 2B. Only four cases with HSPB1 mutations have been reported to date in Japan. In this study between April 2007 and October 2014, we conducted gene panel sequencing in a case series of 1,030 patients with inherited peripheral neuropathies (IPNs) using DNA microarray, targeted resequencing, and whole-exome sequencing. We identified HSPB1 variants in 1.3 % (13 of 1,030) of the patients with IPNs, who exhibited a male predominance. Based on neurological and electrophysiological findings, seven patients were diagnosed with CMT disease type 2F, whereas the remaining six patients were diagnosed with distal hereditary motor neuropathy type 2B. P39L, R127W, S135C, R140G, K141Q, T151I, and P182A mutations identified in 12 patients were described previously, whereas a novel K123* variant with unknown significance was found in one patient. Diabetes and impaired glucose tolerance were detected in 6 of the 13 patients. Our findings suggest that HSPB1 mutations result in two phenotypes of inherited neuropathies and extend the phenotypic spectrum of HSPB1-related disorders.

PMID: 29381233 [PubMed - as supplied by publisher]

Biallelic CHP1 mutation causes human autosomal recessive ataxia by impairing NHE1 function.

Neurol Genet. 2018 Feb;4(1):e209

Authors: Mendoza-Ferreira N, Coutelier M, Janzen E, Hosseinibarkooie S, Löhr H, Schneider S, Milbradt J, Karakaya M, Riessland M, Pichlo C, Torres-Benito L, Singleton A, Zuchner S, Brice A, Durr A, Hammerschmidt M, Stevanin G, Wirth B

Abstract
Objective: To ascertain the genetic and functional basis of complex autosomal recessive cerebellar ataxia (ARCA) presented by 2 siblings of a consanguineous family characterized by motor neuropathy, cerebellar atrophy, spastic paraparesis, intellectual disability, and slow ocular saccades.
Methods: Combined whole-genome linkage analysis, whole-exome sequencing, and focused screening for identification of potential causative genes were performed. Assessment of the functional consequences of the mutation on protein function via subcellular fractionation, size-exclusion chromatography, and fluorescence microscopy were done. A zebrafish model, using Morpholinos, was generated to study the pathogenic effect of the mutation in vivo.
Results: We identified a biallelic 3-bp deletion (p.K19del) in CHP1 that cosegregates with the disease. Neither focused screening for CHP1 variants in 2 cohorts (ARCA: N = 319 and NeurOmics: N = 657) nor interrogating GeneMatcher yielded additional variants, thus revealing the scarcity of CHP1 mutations. We show that mutant CHP1 fails to integrate into functional protein complexes and is prone to aggregation, thereby leading to diminished levels of soluble CHP1 and reduced membrane targeting of NHE1, a major Na+/H+ exchanger implicated in syndromic ataxia-deafness. Chp1 deficiency in zebrafish, resembling the affected individuals, led to movement defects, cerebellar hypoplasia, and motor axon abnormalities, which were ameliorated by coinjection with wild-type, but not mutant, human CHP1 messenger RNA.
Conclusions: Collectively, our results identified CHP1 as a novel ataxia-causative gene in humans, further expanding the spectrum of ARCA-associated loci, and corroborated the crucial role of NHE1 within the pathogenesis of these disorders.

PMID: 29379881 [PubMed]

Effect of Whole Exome Sequencing in Diagnosis of Inborn Errors of Metabolism and Neurogenetic Disorders.

Iran J Child Neurol. 2018;12(1):7-15

Authors: Shakiba M, Keramatipour M

Abstract
Objective: Inborn errors of metabolism are complex disorders with huge variability in clinical manifestations. Decreasing cost of whole exome sequencing (WES) in recent years, made it affordable. Therefore, we witnessed an increase in using WES in diagnosis of genetic diseases, including inherited metabolic disorders.
Methods: A systematic search was done in well-known databases including Medline, Google, Cochrane, and PubMed until 1 Oct 2017. We reviewed the articles addressing the use of WES in diagnosis of metabolic and neurogenetic diseases to evaluate its impact in diagnosis of these conditions.
Results: WES is an effective technology with remarkable impact in diagnosis of metabolic and neurologic diseases, especially in complex cases. Diagnostic yield of WES for these conditions has large variety, ranging from 16% to 68% with an increase during recent years. WES can provide fresh valuable information about new disease, new variants and phenotypes. Careful analysis and interpretation of data obtained by WES and precise evaluation of correlation between clinical manifestation and WES findings are necessary to achieve a correct diagnosis.
Conclusion: WES is effective and useful technology for diagnosis of metabolic and neurogenetic diseases, especially in complex or unsolved cases.

PMID: 29379558 [PubMed]

Whole exome sequencing reveals a stop-gain mutation of PKD2 in an autosomal dominant polycystic kidney disease family complicated with aortic dissection.

BMC Med Genet. 2018 Jan 30;19(1):19

Authors: Zhang W, Han Q, Liu Z, Zhou W, Cao Q, Zhou W

Abstract
BACKGROUND: Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited kidney disorder characterized by progressive cyst formation and expansion in the kidneys, which culminates in end-stage renal disease. Aortic dissection is a rare vascular complication of ADPKD and related literature is currently limited.
CASE PRESENTATION: In this report, we described a patient with asymptomatic Stanford B aortic dissection. Further investigation revealed a positive family history of ADPKD and normal renal function. Whole exome sequencing identified a stop-gain mutation c.1774C > T, p.Arg592Ter in the PKD2 gene that segregated in the family. To our knowledge, this is the first report of ADPKD complicated with aortic dissection caused by PKD2 mutation.
CONCLUSIONS: The case illustrates the importance of aorta imaging and molecular diagnosis in ADPKD patients in order to achieve early recognition of the deadly vascular complication.

PMID: 29378535 [PubMed - in process]

Mutational landscape of EGFR-, MYC-, and Kras-driven genetically engineered mouse models of lung adenocarcinoma.

Proc Natl Acad Sci U S A. 2016 10 18;113(42):E6409-E6417

Authors: McFadden DG, Politi K, Bhutkar A, Chen FK, Song X, Pirun M, Santiago PM, Kim-Kiselak C, Platt JT, Lee E, Hodges E, Rosebrock AP, Bronson RT, Socci ND, Hannon GJ, Jacks T, Varmus H

Abstract
Genetically engineered mouse models (GEMMs) of cancer are increasingly being used to assess putative driver mutations identified by large-scale sequencing of human cancer genomes. To accurately interpret experiments that introduce additional mutations, an understanding of the somatic genetic profile and evolution of GEMM tumors is necessary. Here, we performed whole-exome sequencing of tumors from three GEMMs of lung adenocarcinoma driven by mutant epidermal growth factor receptor (EGFR), mutant Kirsten rat sarcoma viral oncogene homolog (Kras), or overexpression of MYC proto-oncogene. Tumors from EGFR- and Kras-driven models exhibited, respectively, 0.02 and 0.07 nonsynonymous mutations per megabase, a dramatically lower average mutational frequency than observed in human lung adenocarcinomas. Tumors from models driven by strong cancer drivers (mutant EGFR and Kras) harbored few mutations in known cancer genes, whereas tumors driven by MYC, a weaker initiating oncogene in the murine lung, acquired recurrent clonal oncogenic Kras mutations. In addition, although EGFR- and Kras-driven models both exhibited recurrent whole-chromosome DNA copy number alterations, the specific chromosomes altered by gain or loss were different in each model. These data demonstrate that GEMM tumors exhibit relatively simple somatic genotypes compared with human cancers of a similar type, making these autochthonous model systems useful for additive engineering approaches to assess the potential of novel mutations on tumorigenesis, cancer progression, and drug sensitivity.

PMID: 27702896 [PubMed - indexed for MEDLINE]

Role of inherited variants in nonsyndromic heart defects confirmed: Broad study identifies variants that cause syndromic disease.

Am J Med Genet A. 2016 Nov;170(11):2763-2764

Authors:

PMID: 27748064 [PubMed - indexed for MEDLINE]

SRRM4 Drives Neuroendocrine Transdifferentiation of Prostate Adenocarcinoma Under Androgen Receptor Pathway Inhibition.

Eur Urol. 2017 Jan;71(1):68-78

Authors: Li Y, Donmez N, Sahinalp C, Xie N, Wang Y, Xue H, Mo F, Beltran H, Gleave M, Wang Y, Collins C, Dong X

Abstract
BACKGROUND: Neuroendocrine prostate cancer (NEPC) is an aggressive subtype of castration-resistant prostate cancer that typically does not respond to androgen receptor pathway inhibition (ARPI), and its diagnosis is increasing.
OBJECTIVE: To understand how NEPC develops and to identify driver genes to inform therapy for NEPC prevention.
DESIGN, SETTING, AND PARTICIPANTS: Whole-transcriptome sequencing data were extracted from prostate tumors from two independent cohorts: The Beltran cohort contained 27 adenocarcinoma and five NEPC patient samples, and the Vancouver Prostate Centre cohort contained three patient samples and nine patient-derived xenografts.
INTERVENTION: A novel bioinformatics tool, comparative alternative splicing detection (COMPAS), was invented to analyze alternative RNA splicing on RNA-sequencing data.
OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: COMPAS identified potential driver genes for NEPC development. Biochemical and biological validations were performed in both prostate cell and tumor models.
RESULTS AND LIMITATION: More than 66% of the splice events were predicted to be regulated by the RNA splicing factor serine/arginine repetitive matrix 4 (SRRM4). In vitro and in vivo evidence confirmed that one SRRM4 target gene was the RE1 silencing transcription factor (REST), a master regulator of neurogenesis. Moreover, SRRM4 strongly stimulated adenocarcinoma cells to express NEPC biomarkers, and this effect was exacerbated by ARPI. ARPI combined with a gain of SRRM4-induced adenocarcinoma cells to assume multicellular spheroid morphology and was essential in establishing progressive NEPC xenografts. These SRRM4 actions were further enhanced by loss of function of TP53.
CONCLUSIONS: SRRM4 drives NEPC progression. This knowledge may guide the development of novel therapeutics aimed at NEPC.
PATIENT SUMMARY: Using next-generation RNA sequencing and our newly developed bioinformatics tool, we identified a neuroendocrine prostate cancer (NEPC)-specific RNA splicing signature that is predominantly controlled by serine/arginine repetitive matrix 4 (SRRM4). We confirmed that SRRM4 drives NEPC progression, and we propose SRRM4 as a potential therapeutic target for NEPC.

PMID: 27180064 [PubMed - indexed for MEDLINE]

Partial growth hormone insensitivity and dysregulatory immune disease associated with de novo germline activating STAT3 mutations.

Mol Cell Endocrinol. 2018 Jan 25;:

Authors: Gutiérrez M, Scaglia P, Keselman A, Martucci L, Karabatas L, Domené S, Martín A, Pennisi P, Blanco M, Sanguineti N, Bezrodnik L, Di Giovanni D, Caldirola MS, Azcoiti ME, Gaillard MI, Denson LA, Zhang K, Husami A, Yayah Jones NH, Hwa V, Revale S, Vázquez M, Jasper H, Kumar A, Domené H

Abstract
Germinal heterozygous activating STAT3 mutations represent a novel monogenic defect associated with multi-organ autoimmune disease and, in some cases, severe growth retardation. By using whole-exome sequencing, we identified two novel STAT3 mutations, p.E616del and p.C426R, in two unrelated pediatric patients with IGF-I deficiency and immune dysregulation. The functional analyses showed that both variants were gain-of-function (GOF), although they were not constitutively phosphorylated. They presented differences in their dephosphorylation kinetics and transcriptional activities under interleukin-6 stimulation. Both variants increased their transcriptional activities in response to growth hormone (GH) treatment. Nonetheless, STAT5b transcriptional activity was diminished in the presence of STAT3 GOF variants, suggesting a disruptive role of STAT3 GOF variants in the GH signaling pathway. This study highlights the broad clinical spectrum of patients presenting activating STAT3 mutations and explores the underlying molecular pathway responsible for this condition, suggesting that different mutations may drive increased activity by slightly different mechanisms.

PMID: 29378236 [PubMed - as supplied by publisher]

Whole exome sequencing identifies a novel homozygous frameshift mutation in the ASPM gene, which causes microcephaly 5, primary, autosomal recessive.

F1000Res. 2017;6:2163

Authors: Bhargav DS, Sreedevi N, Swapna N, Vivek S, Kovvali S

Abstract
Microcephaly is a genetically heterogeneous disorder and is one of the frequently notable conditions in paediatric neuropathology which exists either as a single entity or in association with other co-morbidities. More than a single gene is implicated in true microcephaly and the list is growing with the recent advancements in sequencing technologies. Using massive parallel sequencing, we identified a novel frame shift insertion in the abnormal spindle-like microcephaly-associated protein gene in a client with true autosomal recessive primary microcephaly.  Exome sequencing in the present case helped in identifying the true cause behind the disease, which helps in the premarital counselling for the sibling to avoid future recurrence of the disorder in the family.

PMID: 29375817 [PubMed]

Exome sequencing of a large family identifies potential candidate genes contributing risk to bipolar disorder.

Gene. 2018 Mar 01;645:119-123

Authors: Zhang T, Hou L, Chen DT, McMahon FJ, Wang JC, Rice JP

Abstract
Bipolar disorder is a mental illness with lifetime prevalence of about 1%. Previous genetic studies have identified multiple chromosomal linkage regions and candidate genes that might be associated with bipolar disorder. The present study aimed to identify potential susceptibility variants for bipolar disorder using 6 related case samples from a four-generation family. A combination of exome sequencing and linkage analysis was performed to identify potential susceptibility variants for bipolar disorder. Our study identified a list of five potential candidate genes for bipolar disorder. Among these five genes, GRID1(Glutamate Receptor Delta-1 Subunit), which was previously reported to be associated with several psychiatric disorders and brain related traits, is particularly interesting. Variants with functional significance in this gene were identified from two cousins in our bipolar disorder pedigree. Our findings suggest a potential role for these genes and the related rare variants in the onset and development of bipolar disorder in this one family. Additional research is needed to replicate these findings and evaluate their patho-biological significance.

PMID: 29248581 [PubMed - indexed for MEDLINE]

Fetal Therapy Model of Myelomeningocele with Three-Dimensional Skin Using Amniotic Fluid Cell-Derived Induced Pluripotent Stem Cells.

Stem Cell Reports. 2017 Jun 06;8(6):1701-1713

Authors: Kajiwara K, Tanemoto T, Wada S, Karibe J, Ihara N, Ikemoto Y, Kawasaki T, Oishi Y, Samura O, Okamura K, Takada S, Akutsu H, Sago H, Okamoto A, Umezawa A

Abstract
Myelomeningocele (MMC) is a congenital disease without genetic abnormalities. Neurological symptoms are irreversibly impaired after birth, and no effective treatment has been reported to date. Only surgical repairs have been reported so far. In this study, we performed antenatal treatment of MMC with an artificial skin using induced pluripotent stem cells (iPSCs) generated from a patient with Down syndrome (AF-T21-iPSCs) and twin-twin transfusion syndrome (AF-TTTS-iPSCs) to a rat model. We manufactured three-dimensional skin with epidermis generated from keratinocytes derived from AF-T21-iPSCs and AF-TTTS-iPSCs and dermis of human fibroblasts and collagen type I. For generation of epidermis, we developed a protocol using Y-27632 and epidermal growth factor. The artificial skin was successfully covered over MMC defect sites during pregnancy, implying a possible antenatal surgical treatment with iPSC technology.

PMID: 28591652 [PubMed - indexed for MEDLINE]

Homozygous deletion of exons 2 and 3 of NPC2 associated with Niemann-Pick disease type C.

Am J Med Genet A. 2016 09;170(9):2486-9

Authors: Hebbar M, Prasada L H, Bhowmik AD, Trujillano D, Shukla A, Chakraborti S, Kandaswamy KK, Rolfs A, Kamath N, Dalal A, Bielas S, Girisha KM

PMID: 27271431 [PubMed - indexed for MEDLINE]

GenIO: a phenotype-genotype analysis web server for clinical genomics of rare diseases.

BMC Bioinformatics. 2018 Jan 27;19(1):25

Authors: Koile D, Cordoba M, de Sousa Serro M, Kauffman MA, Yankilevich P

Abstract
BACKGROUND: GenIO is a novel web-server, designed to assist clinical genomics researchers and medical doctors in the diagnostic process of rare genetic diseases. The tool identifies the most probable variants causing a rare disease, using the genomic and clinical information provided by a medical practitioner. Variants identified in a whole-genome, whole-exome or target sequencing studies are annotated, classified and filtered by clinical significance. Candidate genes associated with the patient's symptoms, suspected disease and complementary findings are identified to obtain a small manageable number of the most probable recessive and dominant candidate gene variants associated with the rare disease case. Additionally, following the American College of Medical Genetics and Genomics and the Association of Molecular Pathology (ACMG-AMP) guidelines and recommendations, all potentially pathogenic variants that might be contributing to disease and secondary findings are identified.
RESULTS: A retrospective study was performed on 40 patients with a diagnostic rate of 40%. All the known genes that were previously considered as disease causing were correctly identified in the final inherit model output lists. In previously undiagnosed cases, we had no additional yield.
CONCLUSION: This unique, intuitive and user-friendly tool to assists medical doctors in the clinical genomics diagnostic process is openly available at https://bioinformatics.ibioba-mpsp-conicet.gov.ar/GenIO/ .

PMID: 29374474 [PubMed - in process]