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Cold Spring Harbor Molecular Case Studies

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https://www.readbyqxmd.com/read/29317428/small-cell-transformation-of-alk-rearranged-non-small-cell-adenocarcinoma-of-the-lung
#1
Agnes Balla, Kenneth J Hampel, Farrah Khan, Dara L Aisner, Nikoletta Sidiropoulos
Anaplastic lymphoma kinase (ALK) gene rearrangements are present in approximately 5% of non-small-cell lung cancers (NSCLCs). These rearrangements occur because of a chromosomal inversion within the short arm of chromosome 2, which results in the formation of the echinoderm microtubule-associated protein-like 4 (EML4)-ALK fusion oncogene. While NSCLC transformation to SCLC is a rare phenomenon described in EGFR mutant cancers primarily after treatment with targeted therapy, it is exceedingly rare in ALK rearranged adenocarcinomas (Toyokawa et al...
January 9, 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29305346/a-de-novo-nonsense-mutation-in-asxl3-shared-by-siblings-with-bainbridge-ropers-syndrome
#2
Daniel C Koboldt, Theresa Mihalic Mosher, Benjamin J Kelly, Emily Sites, Dennis Bartholomew, Scott E Hickey, Kim McBride, Richard K Wilson, Peter White
Two sisters (ages 16 y. and 15 y.) have been followed by our clinical genetics team for several years. Both girls have severe intellectual disability, hypotonia, seizures, and distinctive craniofacial features. The parents are healthy, and have no other children. Oligo array, fragile X testing, and numerous single-gene tests were negative. All four family members underwent research exome sequencing, which revealed a heterozygous nonsense mutation in ASXL3 (p.R1036X) that segregated with disease. Exome data and independent Sanger sequencing confirmed that the variant is de novo, suggesting possible germline mosaicism in one parent...
January 5, 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29258992/late-diagnosis-of-a-truncating-wisp3-mutation-results-in-a-severe-phenotype-of-progressive-pseudorheumatoid-dysplasia
#3
Salem Alawbathani, Amit Kawalia, Mert Karakaya, Janine Altmueller, Peter Nuernberg, Sebahattin Cirak
Rare diseases are often misdiagnosed or receive a delayed diagnosis and thus unfortunately affected individuals may not receive optimal medical management. Here, we report a case of two siblings with a severe phenotype of progressive pseudorheumatoid dysplasia (PPD). Their onset of symptoms began at the age of 3 years. Both were neglected in the past and the patients presented with a very severe phenotype and unmitigated natural history. PPD is a rare autosomal recessive skeletal dysplasia characterized by progressive joint stiffness, swelling and pain...
December 19, 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29212833/personalized-cancer-therapy-leveraging-a-knowledge-base-for-clinical-decision-making
#4
Ecaterina Ileana Dumbrava, Funda Meric-Bernstam
The next-generation sequencing (NGS), also known as massively parallel sequencing, is rapidly being incorporated into oncology practice. With increasing numbers of genes tested, interpretation of genomic reports and selecting treatments based on the tumor's genomic analysis becomes more and more complicated for the treating oncologist. To help guide personalized treatments in oncology, The Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy (IPCT) at MD Anderson Cancer Center has developed a knowledge base, available at https://personalizedcancertherapy...
December 6, 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29167286/a-novel-prrt2-pathogenic-variant-in-a-family-with-paroxysmal-kinesigenic-dyskinesia-and-benign-familial-infantile-seizures
#5
Jacqueline G Lu, Juliet Bishop, Sarah Cheyette, Igor B Zhulin, Su Guo, Nara Sobreira, Steven E Brenner
Paroxysmal Kinesigenic Dyskinesia (PKD) is a rare neurological disorder characterized by recurrent attacks of dyskinetic movements without alteration of consciousness that are often triggered by the initiation of voluntary movements. Whole exome sequencing has revealed a cluster of pathogenic variants in PRRT2 (proline-rich transmembrane protein), a gene with a function in synaptic regulation that remains poorly understood. Here, we report the discovery of a novel PRRT2 pathogenic variant inherited in an autosomal dominant pattern in a family with PKD and Benign Familial Infantile Seizures (BFIS)...
November 22, 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29092958/wisp3-mutation-associated-with-pseudorheumatoid-dysplasia
#6
M Reza Sailani, James Chappell, Jingga Inlora, Linnea Lynch, Anil Narasimha, Safoura Mazroui, Amin Zia, Jonathan Bernstein, Omid Aryani, Michael P Snyder
Progressive pseudorheumatoid dysplasia (PPD) is a skeletal dysplasia characterized by predominant involvement of articular cartilage with progressive joint stiffness. Here we report genetic characterization of a consanguineous family segregating an uncharacterized from of skeletal dysplasia. Whole exome sequencing of four affected siblings and their parents identified a loss of function homozygous mutation in the WISP3 gene, leading to diagnosis of PPD in the affected individuals. The identified variant (chr6: 112382301; WISP3:c...
November 1, 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29092957/molecular-characterisation-of-metastatic-pancreatic-neuroendocrine-tumours-pnets-using-whole-genome-and-transcriptome-sequencing
#7
Hui-Li Wong, Kevin C Yang, Yaoqing Shen, Eric Y Zhao, Jonathan M Loree, Hagen F Kennecke, Steve E Kalloger, Joanna M Karasinska, Howard J Lim, Andrew J Mungall, Xiaolan Feng, Janine M Davies, Kasmintan Schrader, Chen Zhou, Aly Karsan, Steven Jm Jones, Janessa Laskin, Marco A Marra, David F Schaeffer, Sharon M Gorski, Daniel J Renouf
Pancreatic neuroendocrine tumours (PNETs) are a genomically and clinically heterogeneous group of pancreatic neoplasms often diagnosed with distant metastases. Recurrent somatic mutations, chromosomal aberrations and gene expression signatures in PNETs have been described, but the clinical significance of these molecular changes is still poorly understood, and the clinical outcomes of PNET patients remain highly variable. To help identify the molecular factors that contribute to PNET progression and metastasis, and as part of an ongoing clinical trial at the BC Cancer Agency (clinicaltrials...
November 1, 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29162654/the-impact-of-hereditary-cancer-gene-panels-on-clinical-care-and-lessons-learned
#8
Volkan Okur, Wendy K Chung
Mutations in hereditary cancer syndromes account for a modest fraction of all cancers; however, identifying patients with these germline mutations offers tremendous health benefits to both patients and their family members. There are about 60 genes that confer a high lifetime risk of specific cancers, and this information can be used to tailor prevention, surveillance, and treatment. With advances in next-generation sequencing technologies and the elimination of gene patents for evaluating genetic information, we are now able to analyze multiple genes simultaneously, leading to the widespread clinical use of gene panels for germline cancer testing...
November 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29162653/de-novo-variants-in-ebf3-are-associated-with-hypotonia-developmental-delay-intellectual-disability-and-autism
#9
Akemi J Tanaka, Megan T Cho, Rebecca Willaert, Kyle Retterer, Yuri A Zarate, Katie Bosanko, Vikki Stefans, Kimihiko Oishi, Amy Williamson, Golder N Wilson, Alice Basinger, Tina Barbaro-Dieber, Lucia Ortega, Susanna Sorrentino, Melissa K Gabriel, Ilse J Anderson, Maria J Guillen Sacoto, Rhonda E Schnur, Wendy K Chung
Using whole-exome sequencing, we identified seven unrelated individuals with global developmental delay, hypotonia, dysmorphic facial features, and an increased frequency of short stature, ataxia, and autism with de novo heterozygous frameshift, nonsense, splice, and missense variants in the Early B-cell Transcription Factor Family Member 3 (EBF3) gene. EBF3 is a member of the collier/olfactory-1/early B-cell factor (COE) family of proteins, which are required for central nervous system (CNS) development. COE proteins are highly evolutionarily conserved and regulate neuronal specification, migration, axon guidance, and dendritogenesis during development and are essential for maintaining neuronal identity in adult neurons...
November 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29162652/elucidating-the-pathogenesis-of-synchronous-and-metachronous-tumors-in-a-woman-with-endometrioid-carcinomas-using-a-whole-exome-sequencing-approach
#10
Ren-Chin Wu, Ema Veras, Jeffrey Lin, Emily Gerry, Asli Bahadirli-Talbott, Alexander Baras, Ayse Ayhan, Ie-Ming Shih, Tian-Li Wang
Synchronous endometrial and ovarian (SEO) carcinomas involve endometrioid neoplasms in both the ovary and uterus at the time of diagnosis. Patients were traditionally classified as having independent primary SEO lesions or as having metastatic endometrioid carcinoma. Recent studies have supported that SEO tumors result from the dissemination of cells from one organ site to another. However, whether this can be considered a "metastasis" or "dissemination" remains unclear. In this report, we performed whole-exome sequencing of tumor samples from a woman with well-differentiated endometrioid SEO tumors and a clinical "recurrent" poorly differentiated peritoneal tumor that was diagnosed 8 years after the complete resection of the SEO tumors...
November 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29042446/clinical-and-metabolic-consequences-of-l-serine-supplementation-in-hereditary-sensory-and-autonomic-neuropathy-type-1c
#11
Mari Auranen, Jussi Toppila, Saranya Suriyanarayanan, Museer A Lone, Anders Paetau, Henna Tyynismaa, Thorsten Hornemann, Emil Ylikallio
Hereditary sensory neuropathy type 1 (HSAN1) may be the first genetic neuropathy amenable to a specific mechanism-based treatment, as L-serine supplementation can be used to lower the neurotoxic levels of 1-deoxysphingolipids (1-deoxySL) that cause the neurodegeneration. The treatment is so far untested in HSAN1C caused by variants in the serine palmitoyl transferase subunit 2 (SPTLC2) gene. The aim of this study was to establish whether oral L-serine lowers 1-deoxySL in a patient with HSAN1C, to perform a dose escalation to find the minimal effective dose, and to assess the safety profile and global metabolic effects of the treatment...
October 17, 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28963436/novel-nr2f1-variants-likely-disrupt-dna-binding-molecular-modeling-in-two-cases-review-of-published-cases-genotype-phenotype-correlation-and-phenotypic-expansion-of-the-bosch-boonstra-schaaf-optic-atrophy-syndrome
#12
Charu Kaiwar, Michael T Zimmerman, Matthew J Ferber, Zhiyv Niu, Raul A Urrutia, Eric W Klee, Dusica Babovic-Vuksanovic
Bosch-Boonstra-Schaaf Optic Atrophy Syndrome (BBSOAS) is a recently described autosomal dominant disorder caused by mutations in NR2F1 gene. There are presently 28 cases of BBSOAS described in the literature. Its common features include developmental delay, intellectual disability, hypotonia, optic nerve atrophy, attention deficit disorder, autism spectrum disorder, seizures, hearing defects, spasticity and thinning of the corpus callosum. Here we report two unrelated probands with novel, de novo, missense variants in NR2F1 The first is a 14-year-old male patient with hypotonia, intellectual disability, optic nerve hypoplasia, delayed bone age, short stature, and altered neurotransmitter levels on CSF testing...
September 28, 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28877932/detection-and-genomic-characterization-of-a-mammary-like-adenocarcinoma
#13
Jasleen K Grewal, Peter Eirew, Martin Jones, Kenrry Chiu, Basile Tessier-Cloutier, Anthony N Karnezis, Aly Karsan, Andy Mungall, Chen Zhou, Stephen Yip, Anna V Tinker, Janessa Laskin, Marco Marra, Steven J M Jones
Whole-genome and transcriptome sequencing were performed to identify potential therapeutic strategies in the absence of viable treatment options for a patient initially diagnosed with vulvar adenocarcinoma. Genomic events were prioritized by comparison against variant distributions in the TCGA pan-cancer dataset, and complemented with detailed transcriptome sequencing and copy number analysis. These findings were considered against published scientific literature in order to evaluate the functional effects of potentially relevant genomic events...
September 6, 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28864462/rapid-whole-genome-sequencing-identifies-a-novel-gabra1-variant-associated-with-west-syndrome
#14
Lauge Farnaes, Shareef A Nahas, Shimul Chowdhury, James Nelson, Serge Batalov, David M Dimmock, Stephen F Kingsmore
A 9-mo-old infant was admitted with infantile spasms that improved on administration of topiramate and steroids. He also had developmental delay, esotropia, and hypsarrhythmia on interictal electroencephalogram (EEG), and normal brain magnetic resonance imaging (MRI). West syndrome is the triad of infantile spasms, interictal hypsarrhythmia, and mental retardation. Rapid trio whole-genome sequencing (WGS) revealed a novel, likely pathogenic, de novo variant in the gene encoding γ-aminobutyric acid (GABA) type A receptor, α1 polypeptide (GABRA1 c...
September 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28864461/somatic-uniparental-disomy-of-chromosome-16p-in-hemimegalencephaly
#15
Nicole G Griffin, Kenneth D Cronin, Nicole M Walley, Christine M Hulette, Gerald A Grant, Mohamad A Mikati, Heather G LaBreche, Catherine W Rehder, Andrew S Allen, Peter B Crino, Erin L Heinzen
Hemimegalencephaly (HME) is a heterogeneous cortical malformation characterized by enlargement of one cerebral hemisphere. Somatic variants in mammalian target of rapamycin (mTOR) regulatory genes have been implicated in some HME cases; however, ∼70% have no identified genetic etiology. Here, we screened two HME patients to identify disease-causing somatic variants. DNA from leukocytes, buccal swabs, and surgically resected brain tissue from two HME patients were screened for somatic variants using genome-wide genotyping arrays or sequencing of the protein-coding regions of the genome...
September 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28864460/a-germline-fanca-alteration-that-is-associated-with-increased-sensitivity-to-dna-damaging-agents
#16
David C Wilkes, Verena Sailer, Hui Xue, Hongwei Cheng, Colin C Collins, Martin Gleave, Yuzhuo Wang, Francesca Demichelis, Himisha Beltran, Mark A Rubin, David S Rickman
Defects in genes involved in DNA damage repair (DDR) pathway are emerging as novel biomarkers and targets for new prostate cancer drug therapies. A previous report revealed an association between an exceptional response to cisplatin treatment and a somatic loss of heterozygosity (LOH) of FANCA in a patient with metastatic prostate cancer who also harbored a germline FANCA variant (S1088F). Although germline FANCA mutations are the most frequent alterations in patients with Fanconi anemia, germline alterations are less common in prostate cancer...
September 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28630369/alpk3-gene-mutation-in-a-patient-with-congenital-cardiomyopathy-and-dysmorphic-features
#17
Ahmet Okay Çağlayan, Rabia Gonul Sezer, Hande Kaymakçalan, Ege Ulgen, Taner Yavuz, Jacob F Baranoski, Abdulkadir Bozaykut, Akdes Serin Harmanci, Yalim Yalcin, Mark W Youngblood, Katsuhito Yasuno, Kaya Bilgüvar, Murat Gunel
Primary cardiomyopathy is one of the most common inherited cardiac diseases and harbors significant phenotypic and genetic heterogeneity. Because of this, genetic testing has become standard in treatment of this disease group. Indeed, in recent years, next-generation DNA sequencing has found broad applications in medicine, both as a routine diagnostic tool for genetic disorders and as a high-throughput discovery tool for identifying novel disease-causing genes. We describe a male infant with primary dilated cardiomyopathy who was diagnosed using intrauterine echocardiography and found to progress to hypertrophic cardiomyopathy after birth...
September 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28619747/successful-immune-checkpoint-blockade-in-a-patient-with-advanced-stage-microsatellite-unstable-biliary-tract-cancer
#18
Elena Czink, Matthias Kloor, Benjamin Goeppert, Stefan Fröhling, Sebastian Uhrig, Tim F Weber, Jörn Meinel, Christian Sutter, Karl Heinz Weiss, Peter Schirmacher, Magnus von Knebel Doeberitz, Dirk Jäger, Christoph Springfeld
Cancers acquire multiple somatic mutations that can lead to the generation of immunogenic mutation-induced neoantigens. These neoantigens can be recognized by the host's immune system. However, continuous stimulation of immune cells against tumor antigens can lead to immune cell exhaustion, which allows uncontrolled outgrowth of tumor cells. Recently, immune checkpoint inhibitors have emerged as a novel approach to overcome immune cell exhaustion and reactivate antitumor immune responses. In particular, antibodies blocking the exhaustion-mediating programmed death receptor (PD-1)/programmed death receptor ligand (PD-L1) pathway have shown clinical efficacy...
September 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28550066/rapid-whole-genome-sequencing-identifies-a-novel-homozygous-npc1-variant-associated-with-niemann-pick-type-c1-disease-in-a-7-week-old-male-with-cholestasis
#19
Amber Hildreth, Kristen Wigby, Shimul Chowdhury, Shareef Nahas, Jaime Barea, Paulina Ordonez, Sergey Batalov, David Dimmock, Stephen Kingsmore
Niemann-Pick type C disease (NPC; OMIM #257220) is an inborn error of intracellular cholesterol trafficking. It is an autosomal recessive disorder caused predominantly by mutations in NPC1 Although characterized as a progressive neurological disorder, it can also cause cholestasis and liver dysfunction because of intrahepatocyte lipid accumulation. We report a 7-wk-old infant who was admitted with neonatal cholestasis, and who was diagnosed with a novel homozygous stop-gain variant in NPC1 by rapid whole-genome sequencing (WGS)...
September 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28550065/exceptional-durable-response-to-everolimus-in-a-patient-with-biphenotypic-breast-cancer-harboring-an-stk11-variant
#20
Christine A Parachoniak, Andrew Rankin, Bernadette Gaffney, Ryan Hartmaier, Dan Spritz, Rachel L Erlich, Vincent A Miller, Deborah Morosini, Phil Stephens, Jeffrey S Ross, John Keech, Juliann Chmielecki
Metastatic triple-negative breast cancer comprises 12%-17% of breast cancers and carries a poor prognosis relative to other breast cancer subtypes. Treatment options in this disease are largely limited to systemic chemotherapy. A majority of clinical studies assessing efficacy of targeted therapeutics (e.g., the mammalian target of rapamycin [mTOR] inhibitor everolimus) in advanced breast cancer patients have not utilized predictive genomic biomarker-based selection and have reported only modest improvement in the clinical outcome relative to standard of care...
September 2017: Cold Spring Harbor Molecular Case Studies
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