Exceptional Response to Temsirolimus in a Metastatic Clear Cell Renal Cell Carcinoma With an Early Novel MTOR-Activating Mutation.

J Natl Compr Canc Netw. 2017 Nov;15(11):1310-1315

Authors: Rodríguez-Moreno JF, Apellaniz-Ruiz M, Roldan-Romero JM, Durán I, Beltrán L, Montero-Conde C, Cascón A, Robledo M, García-Donas J, Rodríguez-Antona C

Abstract
mTOR pathway inhibitors are important drugs for the treatment of advanced renal cell carcinoma (RCC). However, no valid predictive markers have been identified to guide treatment selection and identify patients who are sensitive to these drugs. Mutations activating the mTOR pathway have been suggested to predict response; however, their predictive value is still unclear. Here, we present the genomic and functional characterization of a patient with metastatic clear cell RCC (ccRCC) who experienced a partial response to temsirolimus after a poor response to 2 previous lines of treatment. At the time of publication, the patient was disease-free 8 years after temsirolimus treatment. Multiregion whole-exome sequencing (WES) on 3 regions of the primary tumor, 1 metastasis, and blood revealed tumor mutations in driver genes in ccRCC: a missense mutation in VHL (p.W88L), a loss-of-function mutation in BAP1 (p.E454Rfs*15), and a novel missense mutation in MTOR (p.Y1974H). The MTOR mutation was present in all tumor regions, with similar allele frequency as the VHL mutation, and in vitro functional assessment of the MTOR variant demonstrated that it increased mTORC1 activity. Consistently, immunohistochemistry in the tumor samples demonstrated increased levels of phospho-S6. In conclusion, multiregion WES identified a novel MTOR mutation acquired early during tumor development as the event leading to a high sensitivity to temsirolimus treatment. This study supports tumor multiregion sequencing to detect truncal mutations in the mTOR pathway to identify patients sensitive to mTOR inhibitors.

PMID: 29118224 [PubMed - in process]

The First Scube3 Mutant Mouse Line with Pleiotropic Phenotypic Alterations.

G3 (Bethesda). 2016 Dec 07;6(12):4035-4046

Authors: Fuchs H, Sabrautzki S, Przemeck GK, Leuchtenberger S, Lorenz-Depiereux B, Becker L, Rathkolb B, Horsch M, Garrett L, Östereicher MA, Hans W, Abe K, Sagawa N, Rozman J, Vargas-Panesso IL, Sandholzer M, Lisse TS, Adler T, Aguilar-Pimentel JA, Calzada-Wack J, Ehrhard N, Elvert R, Gau C, Hölter SM, Micklich K, Moreth K, Prehn C, Puk O, Racz I, Stoeger C, Vernaleken A, Michel D, Diener S, Wieland T, Adamski J, Bekeredjian R, Busch DH, Favor J, Graw J, Klingenspor M, Lengger C, Maier H, Neff F, Ollert M, Stoeger T, Yildirim AÖ, Strom TM, Zimmer A, Wolf E, Wurst W, Klopstock T, Beckers J, Gailus-Durner V, Hrabé de Angelis M

Abstract
The vertebrate Scube (Signal peptide, CUB, and EGF-like domain-containing protein) family consists of three independent members, Scube1-3, which encode secreted cell surface-associated membrane glycoproteins. Limited information about the general function of this gene family is available, and their roles during adulthood. Here, we present the first Scube3 mutant mouse line (Scube3(N294K/N294K)), which clearly shows phenotypic alterations by carrying a missense mutation in exon 8, and thus contributes to our understanding of SCUBE3 functions. We performed a detailed phenotypic characterization in the German Mouse Clinic (GMC). Scube3(N294K/N294K) mutants showed morphological abnormalities of the skeleton, alterations of parameters relevant for bone metabolism, changes in renal function, and hearing impairments. These findings correlate with characteristics of the rare metabolic bone disorder Paget disease of bone (PDB), associated with the chromosomal region of human SCUBE3 In addition, alterations in energy metabolism, behavior, and neurological functions were detected in Scube3(N294K/N294K) mice. The Scube3(N294K/N294K) mutant mouse line may serve as a new model for further studying the effect of impaired SCUBE3 gene function.

PMID: 27815347 [PubMed - indexed for MEDLINE]

Whole exome sequencing in thrombophilic pedigrees to identify genetic risk factors for venous thromboembolism.

PLoS One. 2017;12(11):e0187699

Authors: Cunha MLR, Meijers JCM, Rosendaal FR, Vlieg AVH, Reitsma PH, Middeldorp S

Abstract
BACKGROUND: Family studies have shown a strong heritability component for venous thromboembolism (VTE), but established genetic risk factors are present in only half of VTE patients.
AIM: To identify genetic risk factors in two large families with unexplained hereditary VTE.
METHODS: We performed whole exome sequencing in 10 affected relatives of two unrelated families with an unexplained tendency for VTE. We prioritized variants shared by all affected relatives from both families, and evaluated these in the remaining affected and unaffected individuals. We prioritized variants based on 3 different filter strategies: variants within candidate genes, rare variants across the exome, and SNPs present in patients with familial VTE and with low frequency in the general population. We used whole exome sequencing data available from 96 unrelated VTE cases with a positive family history of VTE from an affected sib study (the GIFT study) to identify additional carriers and compared the risk-allele frequencies with the general population. Variants found in only one individual were also retained for further analysis. Finally, we assessed the association of these variants with VTE in a population-based case-control study (the MEGA study) with 4,291 cases and 4,866 controls.
RESULTS: Six variants remained as putative disease-risk candidates. These variants are located in 6 genes spread among 3 different loci: 2p21 (PLEKHH2 NM_172069:c.3105T>C, LRPPRC rs372371276, SRBD1 rs34959371), 5q35.2 (UNC5A NM_133369.2:c.1869+23C>A), and 17q25.1 (GPRC5C rs142232982, RAB37 rs556450784). In GIFT, additional carriers were identified only for the variants located in the 2p21 locus. In MEGA, additional carriers for several of these variants were identified in both cases and controls, without a difference in prevalence; no carrier of the UNC5A variant was present.
CONCLUSION: Despite sequencing of several individuals from two thrombophilic families resulting in 6 candidate variants, we were unable to confirm their relevance as novel thrombophilic defects.

PMID: 29117201 [PubMed - in process]

Recessive Distal Motor Neuropathy with Pyramidal signs in an Omani Kindred: Underlying Novel Mutation in the SIGMAR1 Gene.

Eur J Neurol. 2017 Nov 08;:

Authors: Nandhagopal R, Meftah D, Al-Kalbani S, Scott P

Abstract
BACKGROUND: Distal hereditary motor neuropathy (dHMN) due to sigma nonopiod intracellular receptor 1 gene (SIGMAR1) mutation (OMIM 601978.0003) is a rare neuromuscular disorder characterized by prominent amyotrophic distal limb weakness and co-existing pyramidal signs initially described in a Chinese family in the recent year. We report an extended consanguineous Omani family segregating dHMN with pyramidal signs in an autosomal recessive pattern and describe a novel mutation in the SIGMAR1 gene underlying this motor phenotype. We also provide an update on the reported phenotypic profile of SIGMAR1 mutations.
METHODS: We utilized homozygosity mapping and whole exome sequencing of leucocyte DNA obtained from three affected members of an Omani family who manifested with a length-dependent motor neuropathy and pyramidal signs.
RESULTS: We identified a novel C>T transition at nucleotide position 238 (c.238C>T) in exon 2 of SIGMAR1 gene. Sanger sequencing and segregation analysis confirmed the presence of two copies of the variant in the affected subjects, unlike the unaffected healthy parents/sibling carrying at most a single copy. The T allele is predicted to cause a truncating mutation (p.Gln80*), likely flagging the mRNA for nonsense mediated decay (NMD) leading to a complete loss of function, thereby potentially contributing to the disease process.
CONCLUSIONS: Our finding expands the spectrum of SIGMAR1 mutations causing recessive dHMN and indicates that this disorder is panethnic. SIGMAR1 mutation should be included in the diagnostic panel of a dHMN, especially if there are co-existing pyramidal signs and autosomal recessive inheritance. This article is protected by copyright. All rights reserved.

PMID: 29115704 [PubMed - as supplied by publisher]

Epistatic interactions between mutations of TACI (TNFRSF13B) and TCF3 result in a severe primary immunodeficiency disorder and systemic lupus erythematosus.

Clin Transl Immunology. 2017 Oct;6(10):e159

Authors: Ameratunga R, Koopmans W, Woon ST, Leung E, Lehnert K, Slade CA, Tempany JC, Enders A, Steele R, Browett P, Hodgkin PD, Bryant VL

Abstract
Common variable immunodeficiency disorders (CVID) are a group of primary immunodeficiencies where monogenetic causes account for only a fraction of cases. On this evidence, CVID is potentially polygenic and epistatic although there are, as yet, no examples to support this hypothesis. We have identified a non-consanguineous family, who carry the C104R (c.310T>C) mutation of the Transmembrane Activator Calcium-modulator and cyclophilin ligand Interactor (TACI, TNFRSF13B) gene. Variants in TNFRSF13B/TACI are identified in up to 10% of CVID patients, and are associated with, but not solely causative of CVID. The proband is heterozygous for the TNFRSF13B/TACI C104R mutation and meets the Ameratunga et al. diagnostic criteria for CVID and the American College of Rheumatology criteria for systemic lupus erythematosus (SLE). Her son has type 1 diabetes, arthritis, reduced IgG levels and IgA deficiency, but has not inherited the TNFRSF13B/TACI mutation. Her brother, homozygous for the TNFRSF13B/TACI mutation, is in good health despite profound hypogammaglobulinemia and mild cytopenias. We hypothesised that a second unidentified mutation contributed to the symptomatic phenotype of the proband and her son. Whole-exome sequencing of the family revealed a de novo nonsense mutation (T168fsX191) in the Transcription Factor 3 (TCF3) gene encoding the E2A transcription factors, present only in the proband and her son. We demonstrate mutations of TNFRSF13B/TACI impair immunoglobulin isotype switching and antibody production predominantly via T-cell-independent signalling, while mutations of TCF3 impair both T-cell-dependent and -independent pathways of B-cell activation and differentiation. We conclude that epistatic interactions between mutations of the TNFRSF13B/TACI and TCF3 signalling networks lead to the severe CVID-like disorder and SLE in the proband.

PMID: 29114388 [PubMed]

Spectrum of germline mutations in smokers and non-smokers in Brazilian non-small-cell lung cancer (NSCLC) patients.

Carcinogenesis. 2017 Oct 26;38(11):1112-1118

Authors: Couto PP, Bastos-Rodrigues L, Schayek H, Melo FM, Lisboa RGC, Miranda DM, Vilhena A, Bale AE, Friedman E, De Marco L

Abstract
Lung cancer (LC) is a leading cause of cancer-related mortality. Although smoking is the major risk factor, ~15% of all cases occur in never-smokers, suggesting that genetic factors play a role in LC predisposition. Indeed, germline mutations in the TP53 gene predispose to multiple cancer types, including LC. To date, few studies compared the somatic and germline mutational profiles of LC cases by smoking status, and none was reported in Brazilians. Whole-exome sequencing (WES) was performed on two pools (seven smokers and six non-smokers) of tumor-derived DNA using the Illumina HiSeq2000 platform. Files from pools were analyzed separately using Ingenuity®Variant AnalysisTM and Mendel,MD. Validation of all candidate variants was performed by Sanger sequencing. Subsequently, validated mutations were analyzed in germline DNA from the same patients and in ethnically matched controls. In addition, a single recurring Brazilian TP53 germline mutation (R337H) was genotyped in 45 non-small-cell lung cancer patients.Four novel germline variants in the ATAD2, AURKA, PTPRD and THBS1 genes were identified exclusively in smoker patients, and four germline missense variants in PLCD1, RAD52, CP and CDC6 genes were identified solely in non-smokers. There were 4/45 (8.9%) germline carriers of the R337H TP53 mutation. In conclusion, the recurring Brazilian TP53 mutation should be genotyped in all non-small-cell lung cancer in Brazil, regardless of smoking status. Distinct pathogenic mutations and novel sequence variants are detected in Brazilian non-small-cell lung cancer patients, by smoking status. The contribution of these sequence variants to LC pathogenesis remains to be further explored.

PMID: 28968711 [PubMed - indexed for MEDLINE]

Frequency of mutations in a large series of clinically ascertained ovarian cancer cases tested on multi-gene panels compared to reference controls.

Gynecol Oncol. 2017 Nov;147(2):375-380

Authors: Lilyquist J, LaDuca H, Polley E, Davis BT, Shimelis H, Hu C, Hart SN, Dolinsky JS, Couch FJ, Goldgar DE

Abstract
OBJECTIVES: Given the lack of adequate screening modalities, knowledge of ovarian cancer risks for carriers of pathogenic alterations in predisposition genes is important for decisions about risk-reduction by salpingo-oophorectomy. We sought to determine which genes assayed on multi-gene panels are associated with ovarian cancer, the magnitude of the associations, and for which clinically meaningful associations could be ruled out.
METHODS: 7768 adult ovarian cancer cases of European ancestry referred to a single clinical testing laboratory underwent multi-gene panel testing for detection of pathogenic alterations in known or suspected ovarian cancer susceptibility genes. A targeted capture approach was employed to assay each of 19 genes for the presence of pathogenic or likely pathogenic alterations. Mutation frequencies in ovarian cancer cases were compared to mutation frequencies in individuals from the Exome Aggregation Consortium (ExAC). Analyses stratified by family and personal history of other cancers and age at diagnosis were also performed.
RESULTS: Significant associations (p<0.001) were identified between alterations in 11 genes and ovarian cancer, with eight of these displaying ≥5-fold increased risk (BRCA1, BRCA2, BRIP1, MSH2, MSH6, RAD51C, RAD51D). Relative risks of ovarian cancer greater than two-fold were also observed for ATM, but could reliably be ruled out for RAD50 and CHEK2.
CONCLUSIONS: These results will inform clinical management of women found to carry pathogenic alterations in genes tested on multi-gene panels. The knowledge that some genes are not associated with OC can reduce concerns of women found to carry pathogenic alterations in those genes.

PMID: 28888541 [PubMed - indexed for MEDLINE]

Whole-exome sequencing for relapse prediction in patients discontinuing TKI treatment in chronic myeloid leukemia.

Leuk Lymphoma. 2016 07;57(7):1503-4

Authors: Abedin S, Platanias LC

PMID: 26915266 [PubMed - indexed for MEDLINE]

State of the Art Update and Next Questions: Acute Myeloid Leukemia.

Clin Lymphoma Myeloma Leuk. 2017 Nov;17(11):703-709

Authors: Sweet K, Lancet J

Abstract
As our general understanding regarding the complex nature of acute myeloid leukemia (AML) is expanding, so is our ability to translate this biological data into clinically relevant information. The use of whole genome and whole exome sequencing has begun to shed light on the importance of a variety of somatic mutations that are frequently identified in AML. In turn, this has allowed the field to incorporate mutational data into prognostic classifications which can guide treatment decisions. Furthermore, minimal residual disease (MRD) monitoring in AML is more commonplace as the prognostic relevance of MRD at various time points during treat is becoming clear. Many novel treatments have recently been approved, or are expected to gain approval in the near future, and this is opening the door to a more personalized approach to the management of AML.

PMID: 29110833 [PubMed - in process]

Identification of a novel genetic locus underlying tremor and dystonia.

Hum Genomics. 2017 Nov 06;11(1):25

Authors: Monies D, Al-Shaar HA, Goljan EA, Al-Younes B, Al-Breacan MMA, Al-Saif MM, Wakil SM, Meyer BF, Khabar KSA, Bohlega S

Abstract
BACKGROUND: Five affected individuals with syndromic tremulous dystonia, spasticity, and white matter disease from a consanguineous extended family covering a period of over 24 years are presented. A positional cloning approach utilizing genome-wide linkage, homozygozity mapping and whole exome sequencing was used for genetic characterization. The impact of a calmodulin-binding transcription activator 2, (CAMTA2) isoform 2, hypomorphic mutation on mRNA and protein abundance was studied using fluorescent reporter expression cassettes. Human brain sub-region cDNA libraries were used to study the expression pattern of CAMTA2 transcript variants.
RESULTS: Linkage analysis and homozygozity mapping localized the disease allele to a 2.1 Mb interval on chromosome 17 with a LOD score of 4.58. Whole exome sequencing identified a G>A change in the transcript variant 2 5'UTR of CAMTA2 that was only 6 bases upstream of the translation start site (c.-6G > A) (NM_001171166.1) and segregated with disease in an autosomal recessive manner. Transfection of wild type and mutant 5'UTR-linked fluorescent reporters showed no impact upon mRNA levels but a significant reduction in the protein fluorescent activity implying translation inhibition.
CONCLUSIONS: Mutation of CAMTA2 resulting in post-transcriptional inhibition of its own gene activity likely underlies a novel syndromic tremulous dystonia.

PMID: 29110692 [PubMed - in process]

Familial early-onset deep venous thrombosis associated with a novel HRG mutation.

Eur J Med Genet. 2017 Nov 03;:

Authors: Luo J, Zhang W, Zeng Q, Zhou W, Cao Q, Zhou W

Abstract
Deep venous thrombosis (DVT) remains a serious clinical problem that affects millions of people worldwide. Some DVT cases are caused by inherited thrombophilia derived from genetic aberrations and several disease-causing genes have been identified so far. Among them, HRG is an uncommon one with limited related reports. Here, we reported on a family with early-onset DVT where acquired risky conditions were excluded. Whole exome sequencing revealed a novel heterozygous single base pair substitution in exon 2 of HRG gene resulting in a conserved residue replacement of the protein (c. C271T, p. P73S). Sanger sequencing confirmed the co-segregation of the mutation and plasma quantification determined circulating protein deficiency. The mutation might therefore impair hemostatic balance by causing reduced circulating HRG level. Our study broadens the mutation spectrum of the HRG gene and underscores the importance of its function in regulating coagulation pathway.

PMID: 29108964 [PubMed - as supplied by publisher]

Exome sequencing identified a novel missense mutation c.464G>A (p.G155D) in Ca(2+)-binding protein 4 (CABP4) in a Chinese pedigree with autosomal dominant nocturnal frontal lobe epilepsy.

Oncotarget. 2017 Oct 03;8(45):78940-78947

Authors: Chen ZH, Wang C, Zhuo MQ, Zhai QX, Chen Q, Guo YX, Zhang YX, Gui J, Tang ZH, Zeng XL

Abstract
The aim of this study was to identify disease-causing gene mutations in a Chinese family affected with autosomal dominant nocturnal frontal lobe epilepsy (ADNFLE), a 4-generation pedigree of 27 members in the Southern Chinese Han population, including 11 individuals diagnosed with ADNFLE. DNA samples were collected from 15 family members, chinese han people, including seven affected and eight unaffected individuals. None of these patients had night blindness or visual disorders. Four affected individuals were screened for mutations using whole-exome sequencing, and 13 potentially interesting mutations shared by all the four affected individuals were validated using the Sanger sequencing method. Only one novel missense mutation c.464G>A (p.G155D) in the CABP4 gene, encoding the neuronal Ca(2+)-binding protein 4 (CaBP4), was present in all seven affected individuals in this family as revealed by PCR with blood DNA samples using CABP4 primers. The mutation was also found in one young unaffected family member, but was absent from 300 unrelated control subjects. The p.G155D mutation, located near the Ca(2+) binding motif EF-hand 1 and the L-type Ca(2+) channel (Cav1.4) binding motif within the N-terminal lobe of CaBP4, is predicted to affect protein function according to the bioinformatics tools PolyPhen-2 and SIFT. These findings suggest that mutations in the CABP4 gene may be linked to ADNFLE.

PMID: 29108277 [PubMed]

Germline PMS2 and somatic POLE exonuclease mutations cause hypermutability of the leading DNA strand in biallelic mismatch repair deficiency syndrome brain tumours.

J Pathol. 2017 Nov;243(3):331-341

Authors: Andrianova MA, Chetan GK, Sibin MK, Mckee T, Merkler D, Narasinga RK, Ribaux P, Blouin JL, Makrythanasis P, Seplyarskiy VB, Antonarakis SE, Nikolaev SI

Abstract
Biallelic mismatch repair deficiency (bMMRD) in tumours is frequently associated with somatic mutations in the exonuclease domains of DNA polymerases POLE or POLD1, and results in a characteristic mutational profile. In this article, we describe the genetic basis of ultramutated high-grade brain tumours in the context of bMMRD. We performed exome sequencing of two second-cousin patients from a large consanguineous family of Indian origin with early onset of high-grade glioblastoma and astrocytoma. We identified a germline homozygous nonsense variant, p.R802*, in the PMS2 gene. Additionally, by genome sequencing of these tumours, we found extremely high somatic mutation rates (237/Mb and 123/Mb), as well as somatic mutations in the proofreading domain of POLE polymerase (p.P436H and p.L424V), which replicates the leading DNA strand. Most interestingly, we found, in both cancers, that the vast majority of mutations were consistent with the signature of POLE exo(-) , i.e. an abundance of C>A and C>T mutations, particularly in special contexts, on the leading strand. We showed that the fraction of mutations under positive selection among mutations in tumour suppressor genes is more than two-fold lower in ultramutated tumours than in other glioblastomas. Genetic analyses enabled the diagnosis of the two consanguineous childhood brain tumours as being due to a combination of PMS2 germline and POLE somatic variants, and confirmed them as bMMRD/POLE exo(-) disorders. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

PMID: 28805995 [PubMed - indexed for MEDLINE]

Genetics of Reproductive Aging from Gonadal Dysgenesis through Menopause.

Semin Reprod Med. 2017 Mar;35(2):147-159

Authors: Desai S, Rajkovic A

Abstract
Reproduction is essential for the survival of the species and is influenced by external factors such as smoking and exposure to chemotherapy as well as chronic disorders such as obesity and autoimmunity. Reproductive senescence, such as menopause, is also dependent on multiple intrinsic genetic factors. Reproductive aging is not isolated from an overall aging process, and several studies strongly support the link between the early age of menopause and mortality. The extreme form of reproductive aging is primary ovarian insufficiency (POI) with prevalence ranging from 1 to 5% of the female population. POI has been shown to have long-term consequences on overall health. POI and age of menopause have a significant hereditary component. The population-based genome-wide association studies have identified 44 genomic loci to associate with age of menopause, and 29 of 44 loci harbor DNA damage response genes. Recent application of whole exome sequencing on carefully selected families with POI has also revealed a significant contribution of DNA damage response genes. The inability to repair the DNA damage in both somatic and germ cells might be a predisposing factor for the link between reproductive and overall aging in a subset of individuals with POI. The aim of this review is to characterize recent advances in the genetics of POI and its link with overall health.

PMID: 28278532 [PubMed - indexed for MEDLINE]

An Application of NGS for Molecular Investigations in Perrault Syndrome: Study of 14 Families and Review of the Literature.

Hum Mutat. 2016 Dec;37(12):1354-1362

Authors: Lerat J, Jonard L, Loundon N, Christin-Maitre S, Lacombe D, Goizet C, Rouzier C, Van Maldergem L, Gherbi S, Garabedian EN, Bonnefont JP, Touraine P, Mosnier I, Munnich A, Denoyelle F, Marlin S

Abstract
Perrault syndrome (PS) is a rare autosomal recessive condition characterized by deafness and gonadic dysgenesis. Recently, mutations in five genes have been identified: C10orf2, CLPP, HARS2, HSD17B4, and LARS2. Probands included are presented with sensorineural deafness associated with gonadic dysgenesis. DNA was sequenced using next-generation sequencing (NGS) with a panel of 35 deafness genes including the five Perrault genes. Exonic variations known as pathogenic mutations or detected with <1% frequency in public databases were extracted and subjected to segregation analysis within each family. Both mutations and low coverage regions were analyzed by Sanger sequencing. Fourteen female index patients were included. The screening in four cases has been extended to four family members presenting with PS phenotype. For four unrelated patients (28.6%), causative mutations were identified: three homozygous mutations in C10orf2, CLPP, and HARS2, and one compound heterozygous mutation in LARS2. Three additional heterozygous mutations in LARS2 and HSD17B4 were found in three independent familial cases. All these missense mutations were verified by Sanger sequencing. Familial segregation analyses confirmed the molecular diagnosis in all cases carrying biallelic mutations. Because of NGS, molecular analysis confirmed the clinical diagnosis of PS in 28.6% of our cohort and four novel mutations were found in four Perrault genes. For the unsolved cases, exome sequencing should be performed to search for a sixth unknown PS gene.

PMID: 27650058 [PubMed - indexed for MEDLINE]

WES/WGS Reporting of Mutations from Cardiovascular "Actionable" Genes in Clinical Practice: A Key Role for UMD Knowledgebases in the Era of Big Databases.

Hum Mutat. 2016 Dec;37(12):1308-1317

Authors: Pinard A, Salgado D, Desvignes JP, Rai G, Hanna N, Arnaud P, Guien C, Martinez M, Faivre L, Jondeau G, Boileau C, Zaffran S, Béroud C, Collod-Béroud G

Abstract
High-throughput next-generation sequencing such as whole-exome and whole-genome sequencing are being rapidly integrated into clinical practice. The use of these techniques leads to the identification of secondary variants for which decisions about the reporting or not to the patient need to be made. The American College of Medical Genetics and Genomics recently published recommendations for the reporting of these variants in clinical practice for 56 "actionable" genes. Among these, seven are involved in Marfan Syndrome And Related Disorders (MSARD) resulting from mutations of the FBN1, TGFBR1 and 2, ACTA2, SMAD3, MYH11 and MYLK genes. Here, we show that mutations collected in UMD databases for MSARD genes (UMD-MSARD) are rarely reported, including the most frequent ones, in global scale initiatives for variant annotation such as the NHLBI GO Exome Sequencing Project (ESP), the Exome Aggregation Consortium (ExAC), and ClinVar. The predicted pathogenic mutations reported in global scale initiatives but absent in locus-specific databases (LSDBs) mainly correspond to rare events. UMD-MSARD databases are therefore the only resources providing access to the full spectrum of known pathogenic mutations. They are the most comprehensive resources for clinicians and geneticists to interpret MSARD-related variations not only primary variants but also secondary variants.

PMID: 27647783 [PubMed - indexed for MEDLINE]

Mini-Exome Coupled to Read-Depth Based Copy Number Variation Analysis in Patients with Inherited Ataxias.

Hum Mutat. 2016 Dec;37(12):1340-1353

Authors: Marelli C, Guissart C, Hubsch C, Renaud M, Villemin JP, Larrieu L, Charles P, Ayrignac X, Sacconi S, Collignon P, Cuntz-Shadfar D, Perrin L, Benarrosh A, Degardin A, Lagha-Boukbiza O, Mutez E, Carlander B, Morales RJ, Gonzalez V, Carra-Dalliere C, Azakri S, Mignard C, Ollagnon E, Pageot N, Chretien D, Geny C, Azulay JP, Tranchant C, Claustres M, Labauge P, Anheim M, Goizet C, Calvas P, Koenig M

Abstract
Next-generation sequencing (NGS) has an established diagnostic value for inherited ataxia. However, the need of a rigorous process of analysis and validation remains challenging. Moreover, copy number variations (CNV) or dynamic expansions of repeated sequence are classically considered not adequately detected by exome sequencing technique. We applied a strategy of mini-exome coupled to read-depth based CNV analysis to a series of 33 patients with probable inherited ataxia and onset <50 years. The mini-exome consisted of the capture of 4,813 genes having associated clinical phenotypes. Pathogenic variants were found in 42% and variants of uncertain significance in 24% of the patients. These results are comparable to those from whole exome sequencing and better than previous targeted NGS studies. CNV and dynamic expansions of repeated CAG sequence were identified in three patients. We identified both atypical presentation of known ataxia genes (ATM, NPC1) and mutations in genes very rarely associated with ataxia (ERCC4, HSD17B4). We show that mini-exome bioinformatics data analysis allows the identification of CNV and dynamic expansions of repeated sequence. Our study confirms the diagnostic value of the proposed genetic analysis strategy. We also provide an algorithm for the multidisciplinary process of analysis, interpretation, and validation of NGS data.

PMID: 27528516 [PubMed - indexed for MEDLINE]

Exome Sequencing identifies LOXL2 mutation as a cause of familial intracranial aneurysm.

World Neurosurg. 2017 Oct 26;:

Authors: Wu Y, Li Z, Shi Y, Chen L, Tan H, Wang Z, Yin C, Liu L, Hu J

Abstract
BACKGROUND: Genetic risk factors can contribute to the etiology of intracranial aneurysms (IAs) and the genetic predisposition of IAs is largely unknown. Our study is aimed to explore the role of rare variation in IA susceptibility.
METHODS: Whole exome sequencing (WES) was performed in a representative family with history of multiple cases of IAs. WES variants were prioritized by various filtering strategies, including frequency, predicted pathogenicity and functional prediction. Further sanger sequencing was performed in additional two families and sporadic IA cases.
RESULTS: After WES and filtering, 15 single nucleotide variants (SNVs) and 3 insertion/deletions (indels) were prioritized in the family. Among them, we selected 5 candidate variants (located in DHRS3, OR2G3, LOXL2, FGL1 and KLC3) by considering known disease genes or ontology association with cardiovascular morphogenesis or other known diseases. Following genotyping results revealed that only c.C133T/p.H45Y in exon 2 of LOXL2 gene was segregated fully with definite IA phenotypes in the family. Moreover, LOXL2 has been reported as a susceptibility gene for intracranial aneurysms.
CONCLUSION: Our investigations result in a conclusion that LOXL2 c.C133T is a pathogenic mutation which is responsible for a fraction of familial intracranial aneurysms.

PMID: 29107163 [PubMed - as supplied by publisher]

Dupuytren's and Ledderhose Diseases in a Family with LMNA-Related Cardiomyopathy and a Novel Variant in the ASTE1 Gene.

Cells. 2017 Nov 01;6(4):

Authors: Zaragoza MV, Nguyen CHH, Widyastuti HP, McCarthy LA, Grosberg A

Abstract
Dupuytren's disease (palmar fibromatosis) involves nodules in fascia of the hand that leads to flexion contractures. Ledderhose disease (plantar fibromatosis) is similar with nodules of the foot. While clinical aspects are well-described, genetic mechanisms are unknown. We report a family with cardiac disease due to a heterozygous LMNA mutation (c.736C>T, p.Gln246Stop) with palmar/plantar fibromatosis and investigate the hypothesis that a second rare DNA variant increases the risk for fibrotic disease in LMNA mutation carriers. The proband and six family members were evaluated for the cardiac and hand/feet phenotypes and tested for the LMNA mutation. Fibroblast RNA studies revealed monoallelic expression of the normal LMNA allele and reduced lamin A/C mRNAs consistent with LMNA haploinsufficiency. A novel, heterozygous missense variant (c.230T>C, p.Val77Ala) in the Asteroid Homolog 1 (ASTE1) gene was identified as a potential risk factor in fibrotic disease using exome sequencing and family studies of five family members: four LMNA mutation carriers with fibromatosis and one individual without the LMNA mutation and no fibromatosis. With a possible role in epidermal growth factor receptor signaling, ASTE1 may contribute to the increased risk for palmar/plantar fibromatosis in patients with Lamin A/C haploinsufficiency.

PMID: 29104234 [PubMed]

Diagnostic yield of targeted gene panel sequencing to identify the genetic etiology of disorders of sex development.

Mol Cell Endocrinol. 2017 Mar 15;444:19-25

Authors: Kim JH, Kang E, Heo SH, Kim GH, Jang JH, Cho EH, Lee BH, Yoo HW, Choi JH

Abstract
Disorders of sex development (DSD) vary phenotypically and are caused by a number of genetic etiologies. This study investigated the genetic etiology of DSD patients using targeted exome sequencing of 67 known DSD-associated genes in humans. This study included 37 patients with 46, XY DSD and seven patients with 46, XX DSD. We identified known pathogenic mutations or deletion in nine (20.5%) patients in the AR, CYP17A1, SRD5A1, and DMRT1/2 genes. Novel variants were identified in nine patients (20.5%) in the AR, ATRX, CYP17A1, CHD7, MAP3K1, NR5A1, and WWOX genes. Among them, four patients harbored pathogenic or likely pathogenic variants, while the remaining five patients (11.4%) had variants of uncertain significance. We were able to make a genetic diagnosis in 29.5% of patients with pathogenic or likely pathogenic mutations. Targeted exome sequencing is an efficient tool to improve the diagnostic yield of DSD, despite its phenotypic and genetic heterogeneity.

PMID: 28130116 [PubMed - indexed for MEDLINE]