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1.
Periklis Makrythanasis Mari Nelis Federico A. Santoni Michel Guipponi Anne Vannier Frédérique Béna Stefania Gimelli Elisavet Stathaki Samia Temtamy André Mégarbané Amira Masri Mona S. Aglan Maha S. Zaki Armand Bottani Siv Fokstuen Lorraine Gwanmesia Konstantinos Aliferis Mariana Bustamante Eduardo Georgios Stamoulis Stavroula Psoni Sofia Kitsiou‐Tzeli Helen Fryssira Emmanouil Kanavakis Nasir Al‐Allawi Abdelaziz Sefiani Sana' Al Hait Siham C. Elalaoui Nadine Jalkh Lihadh Al‐Gazali Fatma Al‐Jasmi Habiba Chaabouni Bouhamed Ebtesam Abdalla David N. Cooper Hanan Hamamy Stylianos E. Antonarakis 《Human mutation》2014,35(10):1203-1210
Rare, atypical, and undiagnosed autosomal‐recessive disorders frequently occur in the offspring of consanguineous couples. Current routine diagnostic genetic tests fail to establish a diagnosis in many cases. We employed exome sequencing to identify the underlying molecular defects in patients with unresolved but putatively autosomal‐recessive disorders in consanguineous families and postulated that the pathogenic variants would reside within homozygous regions. Fifty consanguineous families participated in the study, with a wide spectrum of clinical phenotypes suggestive of autosomal‐recessive inheritance, but with no definitive molecular diagnosis. DNA samples from the patient(s), unaffected sibling(s), and the parents were genotyped with a 720K SNP array. Exome sequencing and array CGH (comparative genomic hybridization) were then performed on one affected individual per family. High‐confidence pathogenic variants were found in homozygosity in known disease‐causing genes in 18 families (36%) (one by array CGH and 17 by exome sequencing), accounting for the clinical phenotype in whole or in part. In the remainder of the families, no causative variant in a known pathogenic gene was identified. Our study shows that exome sequencing, in addition to being a powerful diagnostic tool, promises to rapidly expand our knowledge of rare genetic Mendelian disorders and can be used to establish more detailed causative links between mutant genotypes and clinical phenotypes. 相似文献
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Tessel Rigter Lidewij Henneman Ulf Kristoffersson Alison Hall Helger G. Yntema Pascal Borry Holger Tönnies Quinten Waisfisz Mariet W. Elting Wybo J. Dondorp Martina C. Cornel 《Human mutation》2013,34(10):1322-1328
High‐throughput nucleotide sequencing (often referred to as next‐generation sequencing; NGS) is increasingly being chosen as a diagnostic tool for cases of expected but unresolved genetic origin. When exploring a higher number of genetic variants, there is a higher chance of detecting unsolicited findings. The consequential increased need for decisions on disclosure of these unsolicited findings poses a challenge for the informed consent procedure. This article discusses the ethical and practical dilemmas encountered when contemplating informed consent for NGS in diagnostics from a multidisciplinary point of view. By exploring recent similar experiences with unsolicited findings in other settings, an attempt is made to describe what can be learned so far for implementing NGS in standard genetic diagnostics. The article concludes with a set of points to consider in order to guide decision‐making on the extent of return of results in relation to the mode of informed consent. We hereby aim to provide a sound basis for developing guidelines for optimizing the informed consent procedure. 相似文献
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Yasutaka Aoki Masamichi Mizuma Tatsuo Hata Takeshi Aoki Yuko Omori Yusuke Ono Yusuke Mizukami Michiaki Unno Toru Furukawa 《The Journal of pathology》2020,251(1):38-48
Intraductal papillary neoplasm of the bile duct (IPNB) is a grossly visible papillary biliary neoplasm with morphological variations and occasional invasion. Recently a new classification of IPNB into type 1 and type 2 was proposed in which the type 1 IPNBs consist of fine papillary neoplastic glands and the type 2 IPNBs consist of complex branching glands, seldom with foci of solid-tubular components. However, clinicopathological and molecular characteristics of these types of IPNBs are yet to be identified. We aimed to uncover clinicopathological and molecular characteristics of the types of IPNBs. Thirty-six IPNBs were studied retrospectively. Clinicopathological features as well as molecular alterations of 31 genes were evaluated by means of targeted next-generation sequencing and immunohistochemical examination of expression of mucin and cancer-associated molecules. The 36 IPNBs were classified into 22 of type 1 and 14 of type 2. The type 1 IPNBs were associated with a non-invasive phenotype, intestinal and oncocytic subtypes, development in the intrahepatic bile duct, overt mucin production, and a relatively good prognosis. The type 2 IPNBs were associated with an invasive phenotype, the pancreatobiliary subtype, development within the extrahepatic bile duct, and worse prognosis compared with the type 1 IPNBs. In the molecular analysis, recurrent mutations were found in TP53 (34.3%), KRAS (31.4%), STK11 (25.7%), CTNNB1 (17.1%), APC (14.3%), SMAD4 (14.3%), GNAS (11.4%), PBRM1 (11.4%), ELF3 (8.6%), KMT2C (8.6%), NF1 (8.6%), PIK3CA (8.6%), ARID1A (5.7%), ARID2 (5.7%), BAP1 (5.7%), BRAF (5.7%), EPHA6 (5.7%), ERBB2 (5.7%), ERBB3 (5.7%), KMT2D (5.7%), and RNF43 (5.7%). Mutations in KRAS and GNAS were enriched in the type 1 IPNBs, whereas mutations in TP53, SMAD4, and KMT2C were enriched in the type 2 IPNBs. These results indicate that IPNBs consist of two distinct types of neoplasms specifically associated with clinicopathological features and molecular phenotypes. © 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. 相似文献
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Mert Karakaya Markus Storbeck Eike A. Strathmann Andrea Delle Vedove Irmgard Hölker Janine Altmueller Leyla Naghiyeva Lea Schmitz‐Steinkrüger Katharina Vezyroglou Susanne Motameny Salem Alawbathani Holger Thiele Ayse Ipek Polat Derya Okur Reza Boostani Ehsan Ghayoor Karimiani Gilbert Wunderlich Didem Ardicli Haluk Topaloglu Janbernd Kirschner Bertold Schrank Reza Maroofian Olafur Magnusson Uluc Yis Peter Nürnberg Raoul Heller Brunhilde Wirth 《Human mutation》2018,39(9):1284-1298
Spinal muscular atrophies (SMAs) are a heterogeneous group of disorders characterized by muscular atrophy, weakness, and hypotonia due to suspected lower motor neuron degeneration (LMND). In a large cohort of 3,465 individuals suspected with SMA submitted for SMN1 testing to our routine diagnostic laboratory, 48.8% carried a homozygous SMN1 deletion, 2.8% a subtle mutation, and an SMN1 deletion, whereas 48.4% remained undiagnosed. Recently, several other genes implicated in SMA/LMND have been reported. Despite several efforts to establish a diagnostic algorithm for non‐5q‐SMA (SMA without deletion or point mutations in SMN1 [5q13.2]), data from large‐scale studies are not available. We tested the clinical utility of targeted sequencing in non‐5q‐SMA by developing two different gene panels. We first analyzed 30 individuals with a small panel including 62 genes associated with LMND using IonTorrent‐AmpliSeq target enrichment. Then, additional 65 individuals were tested with a broader panel encompassing up to 479 genes implicated in neuromuscular diseases (NMDs) with Agilent‐SureSelect target enrichment. The NMD panel provided a higher diagnostic yield (33%) than the restricted LMND panel (13%). Nondiagnosed cases were further subjected to exome or genome sequencing. Our experience supports the use of gene panels covering a broad disease spectrum for diseases that are highly heterogeneous and clinically difficult to differentiate. 相似文献
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Monoclonal antibody discovery and engineering is a field that has traditionally been dominated by high‐throughput screening platforms (e.g. hybridomas and surface display). In recent years the emergence of high‐throughput sequencing has made it possible to obtain large‐scale information on antibody repertoire diversity. Additionally, it has now become more routine to perform high‐throughput sequencing on antibody repertoires to also directly discover antibodies. In this review, we provide an overview of the progress in this field to date and show how high‐throughput screening and sequencing are converging to deliver powerful new workflows for monoclonal antibody discovery and engineering. 相似文献
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T. Rigter C.J.A. van Aart M.W. Elting Q. Waisfisz M.C. Cornel L. Henneman 《Clinical genetics》2014,85(5):417-422
Next‐generation sequencing is increasingly being chosen as a diagnostic tool for cases of expected genetic, but unresolved origin. The consequential increased need for decisions on disclosure of unsolicited findings poses a challenge for the informed consent procedure. This study explored the first experiences with, and needs for, the informed consent procedure in diagnostic exome sequencing, with the stakeholders involved. Semi‐structured interviews were conducted with 11 professional experts and one professional gave a written response. Furthermore, the counseling process was observed in three cases where exome sequencing was offered, followed by interviews with the patient (representative) and the genetic counselor. The respondents not only preferred an opt‐out for unsolicited findings but also identified many challenges and therefore more experiences with exome sequencing was considered needed. Context‐dependent decision‐making was observed and an Advisory Board for unsolicited findings was considered helpful while doubts were raised about the feasibility and the possibility of undermining patients' autonomy. Finally, respondents brought up the complexity of information provision, and division of responsibilities between clinicians and the lab. These challenges and needs, raised by stakeholders involved, provide more insight in the next steps needed for an optimal informed consent procedure for exome sequencing in diagnostics. 相似文献
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M. Ishida T. Cullup C. Boustred C. James J. Docker C. English GOSgene N. Lench A.J. Copp G.E. Moore N.D.E. Greene P. Stanier 《Clinical genetics》2018,93(4):870-879
Neural tube defects (NTDs) affecting the brain (anencephaly) are lethal before or at birth, whereas lower spinal defects (spina bifida) may lead to lifelong neurological handicap. Collectively, NTDs rank among the most common birth defects worldwide. This study focuses on anencephaly, which despite having a similar frequency to spina bifida and being the most common type of NTD observed in mouse models, has had more limited inclusion in genetic studies. A genetic influence is strongly implicated in determining risk of NTDs and a molecular diagnosis is of fundamental importance to families both in terms of understanding the origin of the condition and for managing future pregnancies. Here we used a custom panel of 191 NTD candidate genes to screen 90 patients with cranial NTDs (n = 85 anencephaly and n = 5 craniorachischisis) with a targeted exome sequencing platform. After filtering and comparing to our in‐house control exome database (N = 509), we identified 397 rare variants (minor allele frequency, MAF < 1%), 21 of which were previously unreported and predicted damaging. This included 1 frameshift (PDGFRA), 2 stop‐gained (MAT1A; NOS2) and 18 missense variations. Together with evidence for oligogenic inheritance, this study provides new information on the possible genetic causation of anencephaly. 相似文献
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Hongzhi Cao Yu Wang Wei Zhang Xianghua Chai Xiandong Zhang Shiping Chen Fan Yang Caifen Zhang Yulai Guo Ying Liu Zhoubiao Tang Caifen Chen Yaxin Xue Hefu Zhen Yinyin Xu Bin Rao Tao Liu Meiru Zhao Wenwei Zhang Yingrui Li Xiuqing Zhang Laurent C. A. M. Tellier Anders Krogh Karsten Kristiansen Jun Wang Jian Li 《Human mutation》2013,34(12):1715-1720
Accurate genotyping is important for genetic testing. Sanger sequencing‐based typing is the gold standard for genotyping, but it has been underused, due to its high cost and low throughput. In contrast, short‐read sequencing provides inexpensive and high‐throughput sequencing, holding great promise for reaching the goal of cost‐effective and high‐throughput genotyping. However, the short‐read length and the paucity of appropriate genotyping methods, pose a major challenge. Here, we present RCHSBT—reliable, cost‐effective and high‐throughput sequence based typing pipeline—which takes short sequence reads as input, but uses a unique variant calling, haploid sequence assembling algorithm, can accurately genotype with greater effective length per amplicon than even Sanger sequencing reads. The RCHSBT method was tested for the human MHC loci HLA‐A, HLA‐B, HLA‐C, HLA‐DQB1, and HLA‐DRB1, upon 96 samples using Illumina PE 150 reads. Amplicons as long as 950 bp were readily genotyped, achieving 100% typing concordance between RCHSBT‐called genotypes and genotypes previously called by Sanger sequence. Genotyping throughput was increased over 10 times, and cost was reduced over five times, for RCHSBT as compared with Sanger sequence genotyping. We thus demonstrate RCHSBT to be a genotyping method comparable to Sanger sequencing‐based typing in quality, while being more cost‐effective, and higher throughput. 相似文献
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Loredana Bury Karyn Megy Jonathan C. Stephens Luigi Grassi Daniel Greene Nick Gleadall Karina Althaus David Allsup Tadbir K. Bariana Mariana Bonduel Nora V. Butta Peter Collins Nicola Curry Sri V. V. Deevi Kate Downes Daniel Duarte Kim Elliott Emanuela Falcinelli Bruce Furie David Keeling Michele P. Lambert Rachel Linger Sarah Mangles Rutendo Mapeta Carolyn M. Millar Christopher Penkett David J. Perry Kathleen E. Stirrups Ernest Turro Sarah K. Westbury John Wu NIHR BioResource Keith Gomez Kathleen Freson Willem H. Ouwehand Paolo Gresele Ilenia Simeoni 《Human mutation》2020,41(1):277-290
The heterogeneous manifestations of MYH9‐related disorder (MYH9‐RD), characterized by macrothrombocytopenia, Döhle‐like inclusion bodies in leukocytes, bleeding of variable severity with, in some cases, ear, eye, kidney, and liver involvement, make the diagnosis for these patients still challenging in clinical practice. We collected phenotypic data and analyzed the genetic variants in more than 3,000 patients with a bleeding or platelet disorder. Patients were enrolled in the BRIDGE‐BPD and ThromboGenomics Projects and their samples processed by high throughput sequencing (HTS). We identified 50 patients with a rare variant in MYH9. All patients had macrothrombocytes and all except two had thrombocytopenia. Some degree of bleeding diathesis was reported in 41 of the 50 patients. Eleven patients presented hearing impairment, three renal failure and two elevated liver enzymes. Among the 28 rare variants identified in MYH9, 12 were novel. HTS was instrumental in diagnosing 23 patients (46%). Our results confirm the clinical heterogeneity of MYH9‐RD and show that, in the presence of an unclassified platelet disorder with macrothrombocytes, MYH9‐RD should always be considered. A HTS‐based strategy is a reliable method to reach a conclusive diagnosis of MYH9‐RD in clinical practice. 相似文献
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Jiwon Koh Soo Kyung Nam Yoonjin Kwak Gilhyang Kim Ka‐Kyung Kim Byung‐Chul Lee Sang‐Hoon Ahn Do Joong Park Hyung‐Ho Kim Kyoung Un Park Woo Ho Kim Hye Seung Lee 《The Journal of pathology》2021,253(1):94-105
We aimed to determine the pathogenesis of gastric mixed adenoneuroendocrine carcinoma (MANEC) and pure neuroendocrine carcinoma (NEC), which is largely unknown. Targeted DNA sequencing was performed on 34 tumor samples from 21 patients – 13 adenocarcinoma (ADC)/NEC components from MANECs and eight pure NECs – and 21 matched non‐neoplastic gastric tissues. Mutational profiles of MANECs/NECs were compared with those of other tumors using public databases. The majority (64.1%; 59/92) of mutations in MANEC were shared by both ADC and NEC components. TP53 was the most commonly mutated gene in MANEC (69.2%, 9/13) and pure NEC (87.5%, 8/9). All TP53 mutations in MANEC were pathogenic mutations and were shared by both ADC and NEC components. A subset of TP53WT MANECs had a microsatellite‐unstable phenotype or amplifications in various oncogenes including ERBB2 and NMYC, and the only TP53WT pure NEC harbored MYC amplification. Compared to NEC in other organs, NECs arising from the stomach had unique features including less frequent RB1 mutations. Differentially altered genes of MANEC ADC components were significantly associated with receptor tyrosine kinase signaling pathways, while differentially altered genes of MANEC NEC components were significantly associated with the NOTCH signaling pathway. Our data provide evidence suggesting a possible clonal origin of ADC and NEC components of MANEC, and we found that gastric MANECs and pure NECs are distinct entities with unique mutational profiles and underlying protein networks. © 2020 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. 相似文献
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Esben B. Madsen Ida Hijer Thomas Kvist Adam Ameur Marie J. Mikkelsen 《Human mutation》2020,41(9):1671-1679
Long‐read sequencing can resolve regions of the genome that are inaccessible to short reads, and therefore are ideal for genome‐gap closure, solving structural rearrangements and sequencing through repetitive elements. Here we introduce the Xdrop technology: a novel microfluidic‐based system that allows for targeted enrichment of long DNA molecules starting from only a few nanograms of DNA. Xdrop is based on the isolation of long DNA fragments in millions of droplets, where the droplets containing a target sequence of interest are fluorescently labeled and sorted using flow cytometry. The final product from the Xdrop procedure is an enriched population of long DNA molecules that can be investigated by sequencing. To demonstrate the capability of Xdrop, we performed enrichment of the human papilloma virus 18 integrated into the genome of human HeLa cells. Analysis of the sequencing reads resolved three HPV18‐chr8 integrations at base‐pair resolution, and the captured fragments extended up to 30 kb into the human genome at the integration sites. Further, we enriched the complete TP53 locus in a leukemia cell line and could successfully phase coexisting mutations using PacBio sequencing. In summary, our results show that Xdrop is an efficient enrichment technology for studying complex genomic regions. 相似文献
14.
VA Arboleda H Lee FJ Sánchez EC Délot DE Sandberg WW Grody SF Nelson E Vilain 《Clinical genetics》2013,83(1):35-43
Arboleda VA, Lee H, Sánchez FJ, Délot EC, Sandberg DE, Grody WW, Nelson SF, Vilain E. Targeted massively parallel sequencing provides comprehensive genetic diagnosis for patients with disorders of sex development. Disorders of sex development (DSD) are rare disorders in which there is discordance between chromosomal, gonadal, and phenotypic sex. Only a minority of patients clinically diagnosed with DSD obtains a molecular diagnosis, leaving a large gap in our understanding of the prevalence, management, and outcomes in affected patients. We created a novel DSD‐genetic diagnostic tool, in which sex development genes are captured using RNA probes and undergo massively parallel sequencing. In the pilot group of 14 patients, we determined sex chromosome dosage, copy number variation, and gene mutations. In the patients with a known genetic diagnosis (obtained either on a clinical or research basis), this test identified the molecular cause in 100% (7/7) of patients. In patients in whom no molecular diagnosis had been made, this tool identified a genetic diagnosis in two of seven patients. Targeted sequencing of genes representing a specific spectrum of disorders can result in a higher rate of genetic diagnoses than current diagnostic approaches. Our DSD diagnostic tool provides for first time, in a single blood test, a comprehensive genetic diagnosis in patients presenting with a wide range of urogenital anomalies. 相似文献
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Bailing Zu Zhigang Wang Yunlan Xu Guoling You Qihua Fu 《Developmental dynamics》2021,250(9):1220-1228
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D. Liang Y. Wang X. Ji H. Hu J. Zhang L. Meng Y. Lin D. Ma T. Jiang H. Jiang Asan L. Song J. Guo P. Hu Z. Xu 《Clinical genetics》2017,91(4):605-610
Individuals carrying balanced translocations have a high risk of birth defects, recurrent spontaneous abortions and infertility. Thus, the detection and characterization of balanced translocations is important to reveal the genetic background of the carriers and to provide proper genetic counseling. Next‐generation sequencing (NGS), which has great advantages over other methods such as karyotyping and fluorescence in situ hybridization (FISH), has been used to detect disease‐associated breakpoints. Herein, to evaluate the application of this technology to detect balanced translocations in the clinic, we performed a parental study for prenatal cases with unbalanced translocations. Eight candidate families with potential balanced translocations were investigated using two strategies in parallel, low‐coverage whole‐genome sequencing (WGS) followed‐up by Sanger sequencing and G‐banding karyotype coupled with FISH. G‐banding analysis revealed three balanced translocations, and FISH detected two cryptic submicroscopic balanced translocations. Consistently, WGS detected five balanced translocations and mapped all the breakpoints by Sanger sequencing. Analysis of the breakpoints revealed that six genes were disrupted in the four apparently healthy carriers. In summary, our result suggested low‐coverage WGS can detect balanced translocations reliably and can map breakpoints precisely compared with conventional procedures. WGS may replace cytogenetic methods in the diagnosis of balanced translocation carriers in the clinic. 相似文献
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Rafael F. Cita Maristela F. Mendes Diones P. Nogueira Tonny L. Souza Vinícius N. Stelet 《HLA》2021,97(1):73-74
Identification of the novel HLA‐B*15:555 allele that differs from HLA‐B*15:17:01 at one position in exon 2. 相似文献
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Jane Halliday Judith Lumley Leslie J. Sheffield Paul A. L. Lancaster 《American journal of medical genetics. Part A》1993,47(7):1096-1098
Record linkage between a prenatal diagnosis register and a congenital malformation register in the state of Victoria, Australia, has enabled further evaluation of the suggested association between limb deficiencies and early chorion villus sampling (CVS). We found 3 anomalies in this category after later CVS (i.e., 9 weeks and beyond), but our data suggest that advanced maternal age may be a risk factor for both terminal and all limb deficiencies. The data from Victoria are tabulated with data obtained from other registers. Different birth prevalence figures are obtained by different registers, therefore limiting comparisons between registers. © 1993 Wiley-Liss, Inc. 相似文献
20.
Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs 总被引：4，自引：0，他引：4
Canonical microRNAs (miRNAs) require two processing steps: the first by the Microprocessor, a complex of DGCR8 and Drosha, and the second by a complex of TRBP and Dicer. dgcr8Delta/Delta mouse embryonic stem cells (mESCs) have less severe phenotypes than dicer1Delta/Delta mESCs, suggesting a physiological role for Microprocessor-independent, Dicer-dependent small RNAs. To identify these small RNAs with unusual biogenesis, we performed high-throughput sequencing from wild-type, dgcr8Delta/Delta, and dicer1Delta/Delta mESCs. Several of the resulting DGCR8-independent, Dicer-dependent RNAs were noncanonical miRNAs. These derived from mirtrons and a newly identified subclass of miRNA precursors, which appears to be the endogenous counterpart of shRNAs. Our analyses also revealed endogenous siRNAs resulting from Dicer cleavage of long hairpins, the vast majority of which originated from one genomic locus with tandem, inverted short interspersed nuclear elements (SINEs). Our results extend the known diversity of mammalian small RNA-generating pathways and show that mammalian siRNAs exist in cell types other than oocytes. 相似文献
