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Whole genome sequencing pathology

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https://www.readbyqxmd.com/read/28542371/whole-genome-sequencing-of-spermatocytic-tumors-provides-insights-into-the-mutational-processes-operating-in-the-male-germline
#1
Eleni Giannoulatou, Geoffrey J Maher, Zhihao Ding, Ad J M Gillis, Lambert C J Dorssers, Alexander Hoischen, Ewa Rajpert-De Meyts, Gilean McVean, Andrew O M Wilkie, Leendert H J Looijenga, Anne Goriely
Adult male germline stem cells (spermatogonia) proliferate by mitosis and, after puberty, generate spermatocytes that undertake meiosis to produce haploid spermatozoa. Germ cells are under evolutionary constraint to curtail mutations and maintain genome integrity. Despite constant turnover, spermatogonia very rarely form tumors, so-called spermatocytic tumors (SpT). In line with the previous identification of FGFR3 and HRAS selfish mutations in a subset of cases, candidate gene screening of 29 SpTs identified an oncogenic NRAS mutation in two cases...
2017: PloS One
https://www.readbyqxmd.com/read/28498920/copy-number-variation-of-functional-rbmy1-is-associated-with-sperm-motility-an-azoospermia-factor-linked-candidate-for-asthenozoospermia
#2
Yuanlong Yan, Xiling Yang, Yunqiang Liu, Ying Shen, Wenling Tu, Qiang Dong, Dong Yang, Yongyi Ma, Yuan Yang
STUDY QUESTION: What is the influence of copy number variation (CNV) in functional RNA binding motif protein Y-linked family 1 (RBMY1) on spermatogenic phenotypes? SUMMARY ANSWER: The RBMY1 functional copy dosage is positively correlated with sperm motility, and dosage insufficiency is an independent risk factor for asthenozoospermia. WHAT IS KNOWN ALREADY: RBMY1, a multi-copy gene expressed exclusively in the adult testis, is one of the most important candidates for male infertility in the azoospermia factor (AZF) region of the Y-chromosome...
May 12, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28494184/current-status-of-research-and-treatment-for-non-small-cell-lung-cancer-in-never-smoking-females
#3
Shin Saito, Fernando Espinoza-Mercado, Hui Liu, Naohiro Sata, Xiaojiang Cui, Harmik J Soukiasian
Lung cancer is the leading cause of cancer-related deaths worldwide with over 1 million deaths each year. The overall prognosis of lung cancer patients remains unsatisfactory, with a 5-year overall survival rate of less than 15%. Although most lung cancers are a result of smoking, approximately 25% of lung cancer cases worldwide are not attributable to tobacco use. Notably, more than half of the lung cancer cases in women occur in non-smokers. Among non-small-cell lung cancer (NSCLC) cases, cigarette-smokers have a greater association with squamous cell carcinoma than adenocarcinoma, which is more common in non-smokers...
May 11, 2017: Cancer Biology & Therapy
https://www.readbyqxmd.com/read/28487883/genetic-and-epigenetic-profiling-of-a-solitary-peutz-jeghers-colon-polyp
#4
Heinz Linhart, Felix Bormann, Barbara Hutter, Benedikt Brors, Frank Lyko
Colon polyps represent precursor lesions of colon cancers and their malignant potential varies according to histological subtype. A rare subtype of colon polyps is the Peutz-Jeghers (PJ) polyp. PJ polyps mostly occur in the context of Peutz-Jeghers syndrome, which is characterized by the development of multiple polyps in the intestinal tract and hyperpigmentation of oral mucosa and lips. Peutz-Jeghers is an autosomal dominant disorder caused by pathogenic variants of the serine threonine kinase STK11. PJ polyps very rarely occur outside of the syndrome and are then referred to as solitary PJ polyps...
May 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28487558/full-genetic-characterization-and-epidemiology-of-a-novel-amdoparvovirus-in-striped-skunk-mephitis-mephitis
#5
Marta Canuti, Hillary E Doyle, Ann P Britton, Andrew S Lang
Amdoparvovirus is a newly defined parvoviral genus that contains four species (Carnivore amdoparvovirus 1-4), including the well-known Aleutian mink disease virus (AMDV). Amdoparvoviruses cause an immune-associated and often lethal wasting syndrome in Mustelidae and Caninae hosts. In this study, we molecularly investigated amdoparvoviruses detected in 44 striped skunks (Mephitis mephitis) found dead in and around Vancouver, British Columbia, Canada. Some of the animals exhibited pathological changes compatible with amdoparvovirus-associated disease...
May 10, 2017: Emerging Microbes & Infections
https://www.readbyqxmd.com/read/28474161/-soft-tissue-tumors-in-hereditary-tumor-syndromes
#6
REVIEW
A Agaimy
Benign and malignant soft tissue tumors usually develop de novo without identifiable risk factors or predisposing conditions. However, in recent decades, soft tissue tumors have been increasingly recognized to be associated with diverse hereditary tumor syndromes as a consequence of germline mutations involving mainly tumor suppressor genes, but rarely also affecting proto-oncogenes. This is mainly the consequence of increasing application of modern genetic analysis tools, such as next-generation sequencing (NGS) and whole genome analyses...
May 4, 2017: Der Pathologe
https://www.readbyqxmd.com/read/28453704/genomic-characterization-of-her2-positive-breast-cancer-and-response-to-neoadjuvant-trastuzumab-and-chemotherapy-results-from-the-acosog-z1041-alliance-trial
#7
R Lesurf, O L Griffith, M Griffith, J Hundal, L Trani, M A Watson, R Aft, M J Ellis, D Ota, V J Suman, F Meric-Bernstam, A M Leitch, J C Boughey, G Unzeitig, A U Buzdar, K K Hunt, E R Mardis
Background: HER2 (ERBB2) gene amplification and its corresponding overexpression are present in 15-30% of invasive breast cancers. While HER2-targeted agents are effective treatments, resistance remains a major cause of death. The American College of Surgeons Oncology Group Z1041 trial (NCT00513292) was designed to compare the pathologic complete response (pCR) rate of distinct regimens of neoadjuvant chemotherapy and trastuzumab, but ultimately identified no difference. Patients and methods: In supplement to tissues from 37 Z1041 cases, 11 similarly treated cases were obtained from a single institution study (NCT00353483)...
May 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28453696/epstein-barr-virus-associated-gastric-cancer-reveals-intratumoral-heterogeneity-of-pik3ca-mutations
#8
C Böger, S Krüger, H M Behrens, S Bock, J Haag, H Kalthoff, C Röcken
Background: Recent whole-genome sequencing identified four molecular subtypes of gastric cancer (GC), of which the subgroup of Epstein-Barr virus-associated GC (EBVaGC) showed a significant enrichment of PIK3CA mutations. We here aimed to validate independently the enrichment of PIK3CA mutations in EBVaGC of a Central European GC cohort, to correlate EBV status with clinico-pathological patient characteristics and to test for a major issue of GC, intratumoral heterogeneity. Patients and methods: In a first step, 484 GCs were screened for EBV and PIK3CA hot spot mutations of exon 9/20 using EBER in situ hybridization and pyrosequencing, respectively...
May 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28414188/a-case-of-splenomegaly-in-cbl-syndrome
#9
Rachel R Coe, Margaret L McKinnon, Maja Tarailo-Graovac, Colin J Ross, Wyeth W Wasserman, Jan M Friedman, Paul C Rogers, Clara D M van Karnebeek
INTRODUCTION: We present a child with unexplained splenomegaly to highlight this feature as a presenting sign of the RASopathy CBL syndrome and to draw attention to the power and utility of next generation genomic sequencing for providing rapid diagnosis and critical information to guide care in the pediatric clinical setting. CLINICAL REPORT: A 7-year-old boy presented with unexplained splenomegaly, attention deficit hyperactivity disorder, mild learning difficulties, easy bruising, mild thrombocytopenia, and subtle dysmorphic features...
April 13, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28404483/anaconda-paramyxovirus-infection-in-an-adult-green-anaconda-after-prolonged-incubation-pathological-characterization-and-whole-genome-sequence-analysis
#10
Patrick C Y Woo, Paolo Martelli, Suk-Wai Hui, Candy C Y Lau, Joseph M Groff, Rachel Y Y Fan, Susanna K P Lau, Kwok-Yung Yuen
From July 2011 to June 2012, 31 out of 33 green anaconda juveniles from an oceanarium in Hong Kong died over a 12-month period. These anacondas were progeny of a female anaconda purchased from Japan and added to the collection in May 2011. The juvenile anacondas were born in July 2011. A novel paramyxovirus, named anaconda paramyxovirus (AnaPV), was isolated from these affected juvenile anacondas. In July 2015, one of the remaining two anacondas, that survived the cluster of fatal infections, died at the age of four...
April 9, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28390408/a-comprehensive-hybridization-model-allows-whole-herv-transcriptome-profiling-using-high-density-microarray
#11
Jérémie Becker, Philippe Pérot, Valérie Cheynet, Guy Oriol, Nathalie Mugnier, Marine Mommert, Olivier Tabone, Julien Textoris, Jean-Baptiste Veyrieras, François Mallet
BACKGROUND: Human endogenous retroviruses (HERVs) have received much attention for their implications in the etiology of many human diseases and their profound effect on evolution. Notably, recent studies have highlighted associations between HERVs expression and cancers (Yu et al., Int J Mol Med 32, 2013), autoimmunity (Balada et al., Int Rev Immunol 29:351-370, 2010) and neurological (Christensen, J Neuroimmune Pharmacol 5:326-335, 2010) conditions. Their repetitive nature makes their study particularly challenging, where expression studies have largely focused on individual loci (De Parseval et al...
April 8, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28383167/hspa8-as-a-novel-fusion-partner-of-nr4a3-in-extraskeletal-myxoid-chondrosarcoma
#12
Milena Urbini, Annalisa Astolfi, Maria Abbondanza Pantaleo, Salvatore Serravalle, Angelo Paolo Dei Tos, Piero Picci, Valentina Indio, Marta Sbaraglia, Stefania Benini, Alberto Righi, Marco Gambarotti, Alessandro Gronchi, Chiara Colombo, Gian Paolo Dagrada, Silvana Pilotti, Roberta Maestro, Maurizio Polano, Maristella Saponara, Giuseppe Tarantino, Andrea Pession, Guido Biasco, Paolo Giovanni Casali, Silvia Stacchiotti
Extraskeletal myxoid chondrosarcoma (EMC) is a very rare sarcoma most often arising in the soft tissue. Rare EMC of the bone have been reported. EMC exhibits distinctive clinico-pathological and genetic features; however, despite the name, it lacks any feature of cartilaginous differentiation. EMC is characterized by the rearrangement of the NR4A3, which, in most cases (about 62-75%), is fused with EWSR1 and less frequently with other partners, including TAF15 (27%), TCF12 (4%), TFG, and FUS. We herein report the identification by whole-transcriptome sequencing of HSPA8 as a novel fusion partner of NR4A3 in a case of EMC...
July 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28375157/isolated-polycystic-liver-disease-genes-define-effectors-of-polycystin-1-function
#13
Whitney Besse, Ke Dong, Jungmin Choi, Sohan Punia, Sorin V Fedeles, Murim Choi, Anna-Rachel Gallagher, Emily B Huang, Ashima Gulati, James Knight, Shrikant Mane, Esa Tahvanainen, Pia Tahvanainen, Simone Sanna-Cherchi, Richard P Lifton, Terry Watnick, York P Pei, Vicente E Torres, Stefan Somlo
Dominantly inherited isolated polycystic liver disease (PCLD) consists of liver cysts that are radiologically and pathologically identical to those seen in autosomal dominant polycystic kidney disease, but without clinically relevant kidney cysts. The causative genes are known for fewer than 40% of PCLD index cases. Here, we have used whole exome sequencing in a discovery cohort of 102 unrelated patients who were excluded for mutations in the 2 most common PCLD genes, PRKCSH and SEC63, to identify heterozygous loss-of-function mutations in 3 additional genes, ALG8, GANAB, and SEC61B...
May 1, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28327926/genomic-characterisation-of-her2-positive-breast-cancer-and-response-to-neoadjuvant-trastuzumab-and-chemotherapy-results-from-the-acosog-z1041-alliance-trial
#14
R Lesurf, O L Griffith, M Griffith, J Hundal, L Trani, M A Watson, R Aft, M J Ellis, D Ota, V J Suman, F Meric-Bernstam, A M Leitch, J C Boughey, G Unzeitig, A U Buzdar, K K Hunt, E R Mardis
Background: HER2 ( ERBB2 ) gene amplification and its corresponding overexpression are present in 15-30% of invasive breast cancers. While HER2-targeted agents are effective treatments, resistance remains a major cause of death. The American College of Surgeons Oncology Group Z1041 trial (NCT00513292) was designed to compare the pathologic complete response (pCR) rate of distinct regimens of neoadjuvant chemotherapy and trastuzumab, but ultimately identified no difference [1]. Patients and methods: In supplement to tissues from 37 Z1041 cases, 11 similarly treated cases were obtained from a single institution study (NCT00353483)...
February 21, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28327142/exome-sequencing-identified-rare-variants-in-genes-hspg2-and-atp2b4-in-a-family-segregating-developmental-dysplasia-of-the-hip
#15
Sulman Basit, Alia M Albalawi, Essa Alharby, Khalid I Khoshhal
BACKGROUND: Developmental dysplasia of the hip (DDH) is a common pathological condition of the musculoskeletal system in infants which results in a congenital and developmental malformation of the hip joint. DDH is a spectrum of pathologies affecting the infant hip ranging from asymptomatic subtle radiographic signs through mild instability to frank dislocations with acetabular dysplasia. A Saudi family with three affected individuals with DDH was identified and genetic analysis was performed to detect the possible genetic defect(s) underlying DDH in the affected members of the family...
March 21, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28323122/exome-analysis-of-the-evolutionary-path-of-hepatocellular-adenoma-carcinoma-transition-vascular-invasion-and-brain-dissemination
#16
Sílvia Vilarinho, E Zeynep Erson-Omay, Kisha Mitchell-Richards, Charles Cha, Carol Nelson-Williams, Akdes Serin Harmancı, Katsuhito Yasuno, Murat Günel, Tamar H Taddei
Hepatocellular adenoma (HCA) is a rare benign liver tumor, predominantly seen in young women. Its major complications are malignant transformation, spontaneous hemorrhage, and rupture. We describe a case of a young female with no underlying liver disease who presented with acute abdominal pain and was found to have a 17cm heterogeneous mass in the left lobe of the liver. She underwent left hepatectomy and pathology revealed a 14cm moderately differentiated hepatocellular carcinoma (HCC) arising in a shell of a HCA...
March 18, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28318500/mutations-in-tmem260-cause-a-pediatric-neurodevelopmental-cardiac-and-renal-syndrome
#17
Asaf Ta-Shma, Tahir N Khan, Asaf Vivante, Jason R Willer, Pavle Matak, Chaim Jalas, Ben Pode-Shakked, Yishay Salem, Yair Anikster, Friedhelm Hildebrandt, Nicholas Katsanis, Orly Elpeleg, Erica E Davis
Despite the accelerated discovery of genes associated with syndromic traits, the majority of families affected by such conditions remain undiagnosed. Here, we employed whole-exome sequencing in two unrelated consanguineous kindreds with central nervous system (CNS), cardiac, renal, and digit abnormalities. We identified homozygous truncating mutations in TMEM260, a locus predicted to encode numerous splice isoforms. Systematic expression analyses across tissues and developmental stages validated two such isoforms, which differ in the utilization of an internal exon...
April 6, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28292896/loss-of-lmod1-impairs-smooth-muscle-cytocontractility-and-causes-megacystis-microcolon-intestinal-hypoperistalsis-syndrome-in-humans-and-mice
#18
Danny Halim, Michael P Wilson, Daniel Oliver, Erwin Brosens, Joke B G M Verheij, Yu Han, Vivek Nanda, Qing Lyu, Michael Doukas, Hans Stoop, Rutger W W Brouwer, Wilfred F J van IJcken, Orazio J Slivano, Alan J Burns, Christine K Christie, Karen L de Mesy Bentley, Alice S Brooks, Dick Tibboel, Suowen Xu, Zheng Gen Jin, Tono Djuwantono, Wei Yan, Maria M Alves, Robert M W Hofstra, Joseph M Miano
Megacystis microcolon intestinal hypoperistalsis syndrome (MMIHS) is a congenital visceral myopathy characterized by severe dilation of the urinary bladder and defective intestinal motility. The genetic basis of MMIHS has been ascribed to spontaneous and autosomal dominant mutations in actin gamma 2 (ACTG2), a smooth muscle contractile gene. However, evidence suggesting a recessive origin of the disease also exists. Using combined homozygosity mapping and whole exome sequencing, a genetically isolated family was found to carry a premature termination codon in Leiomodin1 (LMOD1), a gene preferentially expressed in vascular and visceral smooth muscle cells...
March 28, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28236343/tarseqqc-quality-control-on-targeted-sequencing-experiments-in-r
#19
Gabriela A Merino, Yanina A Murua, Cristóbal Fresno, Juan M Sendoya, Mariano Golubicki, Soledad Iseas, Mariana Coraglio, Osvaldo L Podhajcer, Andrea S Llera, Elmer A Fernández
Targeted sequencing (TS) is growing as a screening methodology used in research and medical genetics to identify genomic alterations causing human diseases. In general, a list of possible genomic variants is derived from mapped reads through a variant calling step. This processing step is usually based on variant coverage, although it may be affected by several factors. Therefore, undercovered relevant clinical variants may not be reported, affecting pathology diagnosis or treatment. Thus, a prior quality control of the experiment is critical to determine variant detection accuracy and to avoid erroneous medical conclusions...
May 2017: Human Mutation
https://www.readbyqxmd.com/read/28235824/a-nonsense-variant-in-the-st14-gene-in-akhal-teke-horses-with-naked-foal-syndrome
#20
Anina Bauer, Theresa Hiemesch, Vidhya Jagannathan, Markus Neuditschko, Iris Bachmann, Stefan Rieder, Sofia Mikko, M Cecilia Penedo, Nadja Tarasova, Martina Vitková, Nicolò Sirtori, Paola Roccabianca, Tosso Leeb, Monika M Welle
Naked foal syndrome (NFS) is a genodermatosis in the Akhal-Teke horse breed. We provide the first scientific description of this phenotype. Affected horses have almost no hair and show a mild ichthyosis. So far, all known NFS affected horses died between a few weeks and 3 yr of age. It is not clear whether a specific pathology caused the premature deaths. NFS is inherited as a monogenic autosomal recessive trait. We mapped the disease causing genetic variant to two segments on chromosomes 7 and 27 in the equine genome...
April 3, 2017: G3: Genes—Genomes—Genetics
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