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Whole genome sequencing pathology

Franziska Hopfner, Dietrich Haubenberger, Wendy R Galpern, Katrina Gwinn, Ashlee Van't Veer, Samantha White, Kailash Bhatia, Charles H Adler, David Eidelberg, William Ondo, Glenn T Stebbins, Caroline M Tanner, Rick C Helmich, Fred A Lenz, Roy V Sillitoe, David Vaillancourt, Jerrold L Vitek, Elan D Louis, Holly A Shill, Matthew P Frosch, Tatiana Foroud, Gregor Kuhlenbäumer, Andrew Singleton, Claudia M Testa, Mark Hallett, Rodger Elble, Günther Deuschl
Essential tremor (ET) is a common cause of significant disability, but its etiologies and pathogenesis are poorly understood. Research has been hampered by the variable definition of ET and by non-standardized research approaches. The National Institute of Neurological Disorders and Stroke (USA) invited experts in ET and related fields to discuss current knowledge, controversies, and gaps in our understanding of ET and to develop recommendations for future research. Discussion focused on phenomenology and phenotypes, therapies and clinical trials, pathophysiology, pathology, and genetics...
October 4, 2016: Parkinsonism & related Disorders
Kattina Zavala, Michael W Vandewege, Federico G Hoffmann, Juan C Opazo
The study of the evolutionary history of genes related to human disease lies at the interface of evolution and medicine. These studies provide the evolutionary context on which medical researchers should work, and are also useful in providing information to suggest further genetic experiments, especially in model species where genetic manipulations can be made. Here we studied the evolution of the β-adrenoreceptor gene family in vertebrates with the aim of adding an evolutionary framework to the already abundant physiological information...
October 18, 2016: General and Comparative Endocrinology
Steven W Barger
Ask any neuroscientist to name the most profound discoveries in the field in the past 60 years, and at or near the top of the list will be a phenomenon or technique related to genes and their expression. Indeed, our understanding of genetics and gene regulation has ushered in whole new systems of knowledge and new empirical approaches, many of which could not have even been imagined prior to the molecular biology boon of recent decades. Neurochemistry, in the classic sense, intersects with these concepts in the manifestation of neuropeptides, obviously dependent upon the central dogma (the established rules by which DNA sequence is eventually converted into protein primary structure) not only for their conformation but also for their levels and locales of expression...
October 17, 2016: Journal of Neurochemistry
Mayuko Furuta, Masaki Ueno, Akihiro Fujimoto, Shinya Hayami, Satoru Yasukawa, Fumiyoshi Kojima, Koji Arihiro, Yoshiiku Kawakami, Christopher P Wardell, Yuichi Shiraishi, Hiroko Tanaka, Kaoru Nakano, Kazuhiro Maejima, Aya Sasaki-Oku, Naoki Tokunaga, Keith A Boroevich, Tetsuo Abe, Hiroshi Aikata, Hideki Ohdan, Kunihito Goto, Michiaki Kubo, Tatsuhiko Tsunoda, Satoru Miyano, Kazuaki Chayama, Hiroki Yamaue, Hidewaki Nakagawa
BACKGROUND & AIMS: Liver cancer has a high risk of multi-centric (MC) occurrence due to a strong carcinogenic background in the liver, in addition to a high risk of intrahepatic metastasis (IM). There are large characteristic differences between IM and MC with regards to their development and clinical outcome, but discriminating between IM and MC is usually non-trivial with respect to clinical or pathological aspects. METHODS: In this study, we performed whole-genome and RNA sequencing analyses of 49 liver nodules and two extra-hepatic metastatic tumors from 23 patients to investigate for any potential to discriminate between IM and MC at the molecular level...
October 11, 2016: Journal of Hepatology
Seow Hoon Saw, Joon Liang Tan, Xin Yue Chan, Kok Gan Chan, Yun Fong Ngeow
BACKGROUND: Meningitis is a major cause of mortality in tuberculosis (TB). It is not clear what factors promote central nervous system invasion and pathology but it has been reported that certain strains of Mycobacterium tuberculosis (Mtb) might have genetic traits associated with neurotropism. METHODS: In this study, we generated whole genome sequences of eight clinical strains of Mtb that were isolated from the cerebrospinal fluid (CSF) of patients presenting with tuberculous meningitis (TBM) in Malaysia, and compared them to the genomes of H37Rv and other respiratory Mtb genomes either downloaded from public databases or extracted from local sputum isolates...
2016: PeerJ
Khaled K Abu-Amero, Arif O Khan, Darren T Oystreck, Altaf A Kondkar, Thomas M Bosley
PURPOSE: To assess the importance of monogenic mutations and chromosomal copy number variants (CNVs) in the occurrence of nonsyndromic bilateral Duane retraction syndrome (bilateral nsDRS). METHODS: The medical records of 12 patients with bilateral nsDRS were reviewed. Genes associated with DRS and associated congenital cranial dysinnervation disorders (SALL4, CHN1, HOXA1, TUBB3, and KIF21A) were sequenced in the standard fashion in each patient. Array comparative genomic hybridization (array CGH) was performed using Affymetrix Cytogenetics Whole-Genome 2...
September 20, 2016: Journal of AAPOS: the Official Publication of the American Association for Pediatric Ophthalmology and Strabismus
Aditya Bagrodia, Byron H Lee, William Lee, Eugene K Cha, John P Sfakianos, Gopa Iyer, Eugene J Pietzak, Sizhi Paul Gao, Emily C Zabor, Irina Ostrovnaya, Samuel D Kaffenberger, Aijazuddin Syed, Maria E Arcila, Raju S Chaganti, Ritika Kundra, Jana Eng, Joseph Hreiki, Vladimir Vacic, Kanika Arora, Dayna M Oschwald, Michael F Berger, Dean F Bajorin, Manjit S Bains, Nikolaus Schultz, Victor E Reuter, Joel Sheinfeld, George J Bosl, Hikmat A Al-Ahmadie, David B Solit, Darren R Feldman
PURPOSE: Owing to its exquisite chemotherapy sensitivity, most patients with metastatic germ cell tumors (GCTs) are cured with cisplatin-based chemotherapy. However, up to 30% of patients with advanced GCT exhibit cisplatin resistance, which requires intensive salvage treatment, and have a 50% risk of cancer-related death. To identify a genetic basis for cisplatin resistance, we performed whole-exome and targeted sequencing of cisplatin-sensitive and cisplatin-resistant GCTs. METHODS: Men with GCT who received a cisplatin-containing chemotherapy regimen and had available tumor tissue were eligible to participate in this study...
September 19, 2016: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
Seung-Hyun Jung, Min Sung Kim, Chan Kwon Jung, Hyun-Chun Park, So Youn Kim, Jieying Liu, Ja-Seong Bae, Sung Hak Lee, Tae-Min Kim, Sug Hyung Lee, Yeun-Jun Chung
Follicular thyroid adenoma (FTA) precedes follicular thyroid carcinoma (FTC) by definition with a favorable prognosis compared to FTC. However, the genetic mechanism of FTA to FTC progression remains unknown. For this, it is required to disclose FTA and FTC genomes in mutational and evolutionary perspectives. We performed whole-exome sequencing and copy number profiling of 14 FTAs and 13 FTCs, which exhibited previously-known gene mutations (NRAS, HRAS, BRAF, TSHR and EIF1AX) and copy number alterations (CNAs) (22q loss and 1q gain) in follicular tumors...
September 9, 2016: Oncotarget
Jillian Casey, Karen Flood, Sean Ennis, Emma Doyle, Michael Farrell, Sally Ann Lynch
OBJECTIVE: To determine the underlying molecular aetiology in a non-consanguineous Irish family who have had three fetal losses because of a primary myopathy characterised by fetal akinesia, arthrogryposis multiplex, bilateral pulmonary hypoplasia and reduced muscle bulk. METHODS: Fetal DNA extracted from amniotic cells was whole genome amplified and subjected to whole exome sequencing. RESULTS: Whole exome sequencing identified compound heterozygous variants in RYR1 as the cause of the lethal myopathy in this family...
September 12, 2016: Prenatal Diagnosis
Annalisa Roberti, Maria Pamela Dobay, Bettina Bisig, David Vallois, Cloé Boéchat, Evripidis Lanitis, Brigitte Bouchindhomme, Marie-Cécile Parrens, Céline Bossard, Leticia Quintanilla-Martinez, Edoardo Missiaglia, Philippe Gaulard, Laurence de Leval
Enteropathy-associated T-cell lymphoma (EATL), a rare and aggressive intestinal malignancy of intraepithelial T lymphocytes, comprises two disease variants (EATL-I and EATL-II) differing in clinical characteristics and pathological features. Here we report findings derived from whole-exome sequencing of 15 EATL-II tumour-normal tissue pairs. The tumour suppressor gene SETD2 encoding a non-redundant H3K36-specific trimethyltransferase is altered in 14/15 cases (93%), mainly by loss-of-function mutations and/or loss of the corresponding locus (3p21...
2016: Nature Communications
Rohini Mehta, Kianoush Jeiran, Aaron B Koenig, Munkzhul Otgonsuren, Zachary Goodman, Ancha Baranova, Zobair Younossi
BACKGROUND: Visceral obesity and metabolic syndrome are commonly associated with non-alcoholic fatty liver disease (NAFLD). The progression of steatosis to NASH depends on a number of metabolic and patient-related factors. The mechanisms of genetic predisposition towards the development of NASH and related fibrosis remain unclear. In this study, our aim was to utilize mitotyping and identify mitochondrial haplotypes that may be associated with NAFLD. METHODS: We examined mitochondrial haplotypes along with patatin-like phospholipase domain containing 3 (PNPLA3) rs738409 genotype to determine their association with NAFLD phenotypes...
2016: BMC Medical Genetics
Jacob L Steenwyk, John S Soghigian, John R Perfect, John G Gibbons
BACKGROUND: Copy number variants (CNVs) are a class of structural variants (SVs) and are defined as fragments of DNA that are present at variable copy number in comparison with a reference genome. Recent advances in bioinformatics methodologies and sequencing technologies have enabled the high-resolution quantification of genome-wide CNVs. In pathogenic fungi SVs have been shown to alter gene expression, influence host specificity, and drive fungicide resistance, but little attention has focused specifically on CNVs...
2016: BMC Genomics
Brooke R Druliner, Shahrooz Rashtak, Xiaoyang Ruan, Taejeong Bae, Nikolaos Vasmatzis, Daniel O'Brien, Ruth Johnson, Donna Felmlee-Devine, Jill Washechek-Aletto, Nivedita Basu, Hongfang Liu, Thomas Smyrk, Alexej Abyzov, Lisa A Boardman
The majority of colorectal cancers (CRCs) arise from adenomatous polyps. In this study, we sought to present the underrecognized CRC with the residual polyp of origin (CRC RPO+) as an entity to be utilized as a model to study colorectal carcinogenesis. We identified all subjects with biopsy-proven CRC RPO+ that were evaluated over 10 years at Mayo Clinic, Rochester, MN, and compared their clinical and pathologic characteristics to CRC without remnant polyps (CRC RPO-). Overall survival and disease-free survival overlap with an equivalent hazard ratio between CRC RPO+ and RPO- cases when age, stage, and grade are adjusted...
August 2016: Translational Oncology
Urs Nydegger, Thomas Lung, Lorenz Risch, Martin Risch, Pedro Medina Escobar, Thomas Bodmer
We work on the assumption that four major specialities or sectors of medical laboratory assays, comprising clinical chemistry, haematology, immunology, and microbiology, embraced by genome sequencing techniques, are routinely in use. Medical laboratory markers for inflammation serve as model: they are allotted to most fields of medical lab assays including genomics. Incessant coding of assays aligns each of them in the long lists of big data. As exemplified with the complement gene family, containing C2, C3, C8A, C8B, CFH, CFI, and ITGB2, heritability patterns/risk factors associated with diseases with genetic glitch of complement components are unfolding...
2016: Mediators of Inflammation
Juan M Rosa-Rosa, Susanna Leskelä, Eva Cristóbal-Lana, Almudena Santón, Ma Ángeles López-García, Gloria Muñoz, Belen Pérez-Mies, Michele Biscuola, Jaime Prat, Oliva E Esther, Robert A Soslow, Xavier Matias-Guiu, Jose Palacios
Undifferentiated and dedifferentiated endometrial carcinomas are rare and highly aggressive subtypes of uterine cancer, not well characterized at a molecular level. To investigate whether dedifferentiated carcinomas carry molecular genetic alterations similar to those of pure undifferentiated carcinomas, and to gain insight into the pathogenesis of these tumors, we selected a cohort of 18 undifferentiated endometrial carcinomas, 8 of them with a well-differentiated endometrioid carcinoma component (dedifferentiated endometrioid carcinomas), and studied them by immunohistochemistry and massive parallel and Sanger sequencing...
August 5, 2016: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
Chao Li, Lei Ding, Chiao-Wang Sun, Li-Chen Wu, Dewang Zhou, Kevin M Pawlik, Alireza Khodadadi-Jamayran, Erik Westin, Frederick D Goldman, Tim M Townes
CRISPR/Cas enhanced correction of the sickle cell disease (SCD) genetic defect in patient-specific induced Pluripotent Stem Cells (iPSCs) provides a potential gene therapy for this debilitating disease. An advantage of this approach is that corrected iPSCs that are free of off-target modifications can be identified before differentiating the cells into hematopoietic progenitors for transplantation. In order for this approach to be practical, iPSC generation must be rapid and efficient. Therefore, we developed a novel helper-dependent adenovirus/Epstein-Barr virus (HDAd/EBV) hybrid reprogramming vector, rCLAE-R6, that delivers six reprogramming factors episomally...
2016: Scientific Reports
Rada G Staneva, L Balabanski, I Dimova, B Rukova, S Hadjidekova, P Dimitrov, V Simeonov, S Ivanov, R Vagarova, M Malinov, R Cukuranovic, V Stefanovic, M Polenakovic, V Djonov, A Galabov, D Toncheva
BEN is a primary, chronic tubulointerstitial nephritis characterized with chronic anemia, absence of edema, xantoderma, normal blood pressure and normal findings on the fundus oculi. The disease is distributed in restricted areas in Bulgaria, Romania, Croatia, Bosnia, Former Yugoslavia. Despite numerous studies on genetic and environmental factors and their possible involvement in BEN, its etiopathogenesis still remains elusive. Our recent study aim to elucidate the possible epigenetic component in BEN development...
2015: Prilozi (Makedonska Akademija Na Naukite i Umetnostite. Oddelenie za Medicinski Nauki)
Katia Hardies, Yiying Cai, Claude Jardel, Anna C Jansen, Mian Cao, Patrick May, Tania Djémié, Caroline Hachon Le Camus, Kathelijn Keymolen, Tine Deconinck, Vikas Bhambhani, Catherine Long, Samin A Sajan, Katherine L Helbig, Arvid Suls, Rudi Balling, Ingo Helbig, Peter De Jonghe, Christel Depienne, Pietro De Camilli, Sarah Weckhuysen
SYNJ1 encodes a polyphosphoinositide phosphatase, synaptojanin 1, which contains two consecutive phosphatase domains and plays a prominent role in synaptic vesicle dynamics. Autosomal recessive inherited variants in SYNJ1 have previously been associated with two different neurological diseases: a recurrent homozygous missense variant (p.Arg258Gln) that abolishes Sac1 phosphatase activity was identified in three independent families with early onset parkinsonism, whereas a homozygous nonsense variant (p.Arg136*) causing a severe decrease of mRNA transcript was found in a single patient with intractable epilepsy and tau pathology...
September 2016: Brain: a Journal of Neurology
Lin Li, Xueya Zhou, Xi Wang, Jing Wang, Wei Zhang, Binbin Wang, Yunxia Cao, Kehkooi Kee
STUDY QUESTION: Does a heterozygous mutation in AMHR2, identified in whole-exome sequencings (WES) of patients with primary ovarian insufficiency (POI), cause a defect in anti-Müllerian hormone (AMH) signaling? SUMMARY ANSWER: The I209N mutation at the adenosine triphosphate binding domain of AMHR2 exerts dominant negative defects in the AMH signaling pathway. WHAT IS KNOWN ALREADY: Previous studies have demonstrated the associations of several sequence variants in AMH or AMHR2 with POI, but no functional assay has been performed to verify whether there was any defect on AMH signaling...
September 2016: Molecular Human Reproduction
Je-Gun Joung, Sang Yun Ha, Joon Seol Bae, Jae-Yong Nam, Geum-Youn Gwak, Hae-Ock Lee, Dae-Soon Son, Cheol-Keun Park, Woong-Yang Park
Dysplastic nodules are premalignant neoplastic nodules found in explanted livers with cirrhosis. Genetic signatures of premalignant dysplastic nodules (DNs) with concurrent hepatocellular carcinoma (HCC) may provide an insight in the molecular evolution of hepatocellular carcinogenesis. We analyzed four patients with multifocal nodular lesions and cirrhotic background by whole-exome sequencing (WES). The genomic profiles of somatic single nucleotide variations (SNV) and copy number variations (CNV) in DNs were compared to those of HCCs...
July 9, 2016: Oncotarget
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