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Cold Spring Harbor Molecular Case Studies

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https://www.readbyqxmd.com/read/28630369/alpk3-gene-mutation-in-a-patient-with-congenital-cardiomyopathy-and-dysmorphic-features
#1
Ahmet Okay Ca─člayan, Rabia Gonul Sezer, Hande Kaymakcalan, Ege Ulgen, Taner Yavuz, Jacob F Baranoski, Abdulkadir Bozaykut, Akdes Serin Harmanci, Yalim Yalcin, Mark W Youngblood, Katsuhito Yasuno, Kaya Bilguvar, 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 also as a high-throughput discovery tool for identifying novel disease causing genes. We describe a male infant with primary dilated cardiomyopathy that was diagnosed using intrauterine echocardiography, and found to progress to hypertrophic cardiomyopathy after birth...
June 19, 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
#2
Elena Czink, Matthias Kloor, Benjamin Goeppert, Stefan Froehling, Sebastian Uhrig, Tim F Weber, Joern Meinel, Christian Sutter, Karl Heinz Weiss, Peter Schirmacher, Magnus von Knebel Doeberitz, Dirk Jaeger, 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 re-activate anti-tumor immune responses. In particular, antibodies blocking the exhaustion-mediating programmed death receptor (PD-1)/PD-L1 pathway have shown clinical efficacy...
June 15, 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
#3
Amber Hildreth, Kristen Wigby, Shimul Chowdhury, Shareef Nahas, Jaime Barea, Paulina Ordonez, Serge Batalov, David M Dimmock, Rcigm Investigators, Stephen F 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. While characterized as a progressive neurological disorder, it can also cause cholestasis and liver dysfunction due to intrahepatocyte lipid accumulation. We report a 7 week old who was admitted with neonatal cholestasis, who was diagnosed with a novel homozygous stop-gain variant in NPC1 by rapid whole genome sequencing (WGS)...
May 26, 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
#4
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 mTOR inhibitor everolimus) in advanced breast cancer patients have not utilized predictive genomic biomarker-based selection and have reported only modest improvement in clinical outcome relative to standard of care...
May 26, 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28514723/genomic-profiling-of-pelvic-genital-type-leiomyosarcoma-in-a-woman-with-a-germline-chek2-c-1100delc-mutation-and-a-concomitant-diagnosis-of-metastatic-invasive-ductal-breast-carcinoma
#5
My Linh Thibodeau, Caralyn Reisle, Eric Zhao, Lee Ann Martin, Yazeed Alwelaie, Karen L Mungall, Carolyn Ch'ng, Ruth Thomas, Tony Ng, Stephen Yip, Howard Lim, Sophie Sun, Sean S Young, Aly Karsan, Yongjun Zhao, Andrew J Mungall, Richard A Moore, Daniel Renouf, Karen Gelmon, Yussanne P Ma, Malcolm Hayes, Janessa Laskin, Marco A Marra, Kasmintan A Schrader, Steven J M Jones
INTRODUCTION: We describe a woman with the known pathogenic germline variant CHEK2:c.1100delC and synchronous diagnoses of both pelvic genital type leiomyosarcoma and metastatic invasive ductal breast carcinoma. CHEK2 (checkpoint kinase 2) is a tumour suppressor gene encoding a serine/threonine-protein kinase (CHEK2) involved in double-strand DNA break repair and cell cycle arrest. The CHEK2:c.1100delC variant is a moderate penetrance allele resulting in an approximate 2-fold increase in breast cancer risk...
May 16, 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28487886/new-tools-and-approaches-to-newborn-screening-ready-to-open-pandora-s-box
#6
Can Ficicioglu
The landscape of newborn screening (NBS) is changing as new tools are developed. We must acknowledge that NBS is a very important and extraordinarily positive initiative especially for rare and serious inherited disorders; however, lessons learned from current NBS should guide the future of NBS as we enter the era of "omics" that will expand NBS for many other genetic disorders. In this article, I will first discuss new tools such as genomics and metabolomics for NBS. I will then turn to assessing how best to take advantage of new technical developments while considering the best interests of patients and the success of newborn screening...
May 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28487885/novel-de-novo-variant-in-ebf3-is-likely-to-impact-dna-binding-in-a-patient-with-a-neurodevelopmental-disorder-and-expanded-phenotypes-patient-report-in-silico-functional-assessment-and-review-of-published-cases
#7
Patrick R Blackburn, Sarah S Barnett, Michael T Zimmermann, Margot A Cousin, Charu Kaiwar, Filippo Pinto E Vairo, Zhiyv Niu, Matthew J Ferber, Raul A Urrutia, Duygu Selcen, Eric W Klee, Pavel N Pichurin
Pathogenic variants in EBF3 were recently described in three back-to-back publications in association with a novel neurodevelopmental disorder characterized by intellectual disability, speech delay, ataxia, and facial dysmorphisms. In this report, we describe an additional patient carrying a de novo missense variant in EBF3 (c.487C>T, p.(Arg163Trp)) that falls within a conserved residue in the zinc knuckle motif of the DNA binding domain. Without a solved structure of the DNA binding domain, we generated a homology-based atomic model and performed molecular dynamics simulations for EBF3, which predicted decreased DNA affinity for p...
May 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28487884/diffuse-large-b-cell-lymphoma-can-genomics-improve-treatment-options-for-a-curable-cancer
#8
REVIEW
Amit Dipak Amin, Tara L Peters, Lingxiao Li, Soumya Sundara Rajan, Ramesh Choudhari, Soham D Puvvada, Jonathan H Schatz
Gene-expression profiling and next-generation sequencing have defined diffuse large B-cell lymphoma (DLBCL), the most common lymphoma diagnosis, as a heterogeneous group of subentities. Despite ongoing explosions of data illuminating disparate pathogenic mechanisms, however, the five-drug chemoimmunotherapy combination R-CHOP remains the frontline standard treatment. This has not changed in 15 years, since the anti-CD20 monoclonal antibody rituximab was added to the CHOP backbone, which first entered use in the 1970s...
May 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28487883/genetic-and-epigenetic-profiling-of-a-solitary-peutz-jeghers-colon-polyp
#9
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/28487882/identification-of-a-novel-rasd1-somatic-mutation-in-a-usp8-mutated-corticotroph-adenoma
#10
Andrew V Uzilov, Khadeen C Cheesman, Marc Y Fink, Leah C Newman, Chetanya Pandya, Yelena Lalazar, Marco Hefti, Mary Fowkes, Gintaras Deikus, Chun Yee Lau, Aye S Moe, Yayoi Kinoshita, Yumi Kasai, Micol Zweig, Arpeta Gupta, Daniela Starcevic, Milind Mahajan, Eric E Schadt, Kalmon D Post, Michael J Donovan, Robert Sebra, Rong Chen, Eliza B Geer
Cushing's disease (CD) is caused by pituitary corticotroph adenomas that secrete excess adrenocorticotropic hormone (ACTH). In these tumors, somatic mutations in the gene USP8 have been identified as recurrent and pathogenic and are the sole known molecular driver for CD. Although other somatic mutations were reported in these studies, their contribution to the pathogenesis of CD remains unexplored. No molecular drivers have been established for a large proportion of CD cases and tumor heterogeneity has not yet been investigated using genomics methods...
May 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28487881/whole-genome-sequencing-identifies-homozygous-brca2-deletion-guiding-treatment-in-dedifferentiated-prostate-cancer
#11
Karin Purshouse, Anna Schuh, Benjamin P Fairfax, Sam Knight, Pavlos Antoniou, Helene Dreau, Niko Popitsch, Kevin Gatter, Ian Roberts, Lisa Browning, Zoe Traill, David Kerr, Clare Verrill, Mark Tuthill, Jenny C Taylor, Andrew Protheroe
Whole-genome sequencing (WGS) has transformed the understanding of the genetic drivers of cancer and is increasingly being used in cancer medicine to identify personalized therapies. Here we describe a case in which the application of WGS identified a tumoral BRCA2 deletion in a patient with aggressive dedifferentiated prostate cancer that was repeat-biopsied after disease progression. This would not have been detected by standard BRCA testing, and it led to additional treatment with a maintenance poly ADP ribose polymerase (PARP) inhibitor following platinum-based chemotherapy...
May 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28487880/when-n-of-2-is-not-enough-integrating-statistical-and-functional-data-in-gene-discovery
#12
Christopher A Cassa, Sebastian Akle, Daniel M Jordan, Jill A Rosenfeld
The expanding use of genomic sequencing promises to improve clinical diagnostics and to drive the discovery of new disease genes. Candidate genes are increasingly being identified through recurrent cases (e.g., two or more independent cases ["N of 2"] in which variants are present in the same gene). These second case hits provide statistical evidence of an association, which may then be combined with functional validation or familial segregation studies to bolster the evidence that a gene is truly causal. Here, we discuss how to integrate different forms of functional evidence with human genetics case and segregation data to improve the significance of new disease-gene associations...
May 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28299359/aifm1-mutation-presenting-with-fatal-encephalomyopathy-and-mitochondrial-disease-in-an-infant
#13
Sarah U Morton, Sanjay P Prabhu, Hart G W Lidov, Jiahai Shi, Irina Anselm, Catherine A Brownstein, Matthew N Bainbridge, Alan H Beggs, Sara O Vargas, Pankaj B Agrawal
Apoptosis-inducing factor mitochondrion-associated 1 (AIFM1), encoded by the gene AIFM1, has roles in electron transport, apoptosis, ferredoxin metabolism, reactive oxygen species generation, and immune system regulation. Here we describe a patient with a novel AIFM1 variant presenting unusually early in life with mitochondrial disease, rapid deterioration, and death. Autopsy, at the age of 4 mo, revealed features of mitochondrial encephalopathy, myopathy, and involvement of peripheral nerves with axonal degeneration...
March 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28299358/a-novel-potentially-targetable-tmem106b-braf-fusion-in-pleomorphic-xanthoastrocytoma
#14
Susan J Hsiao, Matthias A Karajannis, Daniel Diolaiti, Mahesh M Mansukhani, Julia Glade Bender, Andrew L Kung, James H Garvin
Pleomorphic xanthoastrocytoma (PXA) is a World Health Organization (WHO) Grade II glioma occurring primarily in children and young adults. Most PXAs harbor the known activating mutation BRAF V600E. We report a case of locally recurrent PXA with anaplastic features in a 10-yr-old female. The PXA was negative by immunohistochemical (IHC) staining for BRAF V600E mutation. Whole-exome and transcriptome sequencing of the tumor confirmed the absence of BRAF V600E, but identified copy-number alterations (including loss of the tumor suppressor CDKN2A) and a novel TMEM106B-BRAF fusion...
March 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28299357/integrating-functional-genomics-to-accelerate-mechanistic-personalized-medicine
#15
Jeffrey W Tyner
The advent of deep sequencing technologies has resulted in the deciphering of tremendous amounts of genetic information. These data have led to major discoveries, and many anecdotes now exist of individual patients whose clinical outcomes have benefited from novel, genetically guided therapeutic strategies. However, the majority of genetic events in cancer are currently undrugged, leading to a biological gap between understanding of tumor genetic etiology and translation to improved clinical approaches. Functional screening has made tremendous strides in recent years with the development of new experimental approaches to studying ex vivo and in vivo drug sensitivity...
March 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28299356/an-exome-sequencing-study-of-moebius-syndrome-including-atypical-cases-reveals-an-individual-with-cfeom3a-and-a-tubb3-mutation
#16
Ronak M Patel, David Liu, Claudia Gonzaga-Jauregui, Shalini Jhangiani, James T Lu, V Reid Sutton, Susan D Fernbach, Mahshid Azamian, Lisa White, Jane C Edmond, Evelyn A Paysse, John W Belmont, Donna Muzny, James R Lupski, Richard A Gibbs, Richard Alan Lewis, Brendan H Lee, Seema R Lalani, Philippe M Campeau
Moebius syndrome is characterized by congenital unilateral or bilateral facial and abducens nerve palsies (sixth and seventh cranial nerves) causing facial weakness, feeding difficulties, and restricted ocular movements. Abnormalities of the chest wall such as Poland anomaly and variable limb defects are frequently associated with this syndrome. Most cases are isolated; however, rare families with autosomal dominant transmission with incomplete penetrance and variable expressivity have been described. The genetic basis of this condition remains unknown...
March 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28050602/exome-sequencing-identifies-de-novo-pathogenic-variants-in-fbn1-and-trps1-in-a-patient-with-a-complex-connective-tissue-phenotype
#17
Diane B Zastrow, Patricia A Zornio, Annika Dries, Jennefer Kohler, Liliana Fernandez, Daryl Waggott, Magdalena Walkiewicz, Christine M Eng, Melanie A Manning, Ellyn Farrelly, Paul G Fisher, Euan A Ashley, Jonathan A Bernstein, Matthew T Wheeler
Here we describe a patient who presented with a history of congenital diaphragmatic hernia, inguinal hernia, and recurrent umbilical hernia. She also has joint laxity, hypotonia, and dysmorphic features. A unifying diagnosis was not identified based on her clinical phenotype. As part of her evaluation through the Undiagnosed Diseases Network, trio whole-exome sequencing was performed. Pathogenic variants in FBN1 and TRPS1 were identified as causing two distinct autosomal dominant conditions, each with de novo inheritance...
January 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28050601/progeroid-syndrome-patients-with-zmpste24-deficiency-could-benefit-when-treated-with-rapamycin-and-dimethylsulfoxide
#18
Baris Akinci, Shireesha Sankella, Christopher Gilpin, Keiichi Ozono, Abhimanyu Garg, Anil K Agarwal
Patients with progeroid syndromes such as mandibuloacral dysplasia, type B (MADB) and restrictive dermopathy (RD) harbor mutations in zinc metalloproteinase (ZMPSTE24), an enzyme essential for posttranslational proteolysis of prelamin A to form mature lamin A. Dermal fibroblasts from these patients show increased nuclear dysmorphology and reduced proliferation; however, the efficacy of various pharmacological agents in reversing these cellular phenotypes remains unknown. In this study, fibroblasts from MADB patients exhibited marked nuclear abnormalities and reduced proliferation that improved upon treatment with rapamycin and dimethylsulfoxide but not with other agents, including farnesyl transferase inhibitors...
January 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28050600/histiocytoid-cardiomyopathy-and-microphthalmia-with-linear-skin-defects-syndrome-phenotypes-linked-by-truncating-variants-in-ndufb11
#19
Gillian Rea, Tessa Homfray, Jan Till, Ferran Roses-Noguer, Rachel J Buchan, Sam Wilkinson, Alicja Wilk, Roddy Walsh, Shibu John, Shane McKee, Fiona J Stewart, Victoria Murday, Robert W Taylor, Michael Ashworth, A John Baksi, Piers Daubeney, Sanjay Prasad, Paul J R Barton, Stuart A Cook, James S Ware
Variants in NDUFB11, which encodes a structural component of complex I of the mitochondrial respiratory chain (MRC), were recently independently reported to cause histiocytoid cardiomyopathy (histiocytoid CM) and microphthalmia with linear skin defects syndrome (MLS syndrome). Here we report an additional case of histiocytoid CM, which carries a de novo nonsense variant in NDUFB11 (ENST00000276062.8: c.262C > T; p.[Arg88*]) identified using whole-exome sequencing (WES) of a family trio. An identical variant has been previously reported in association with MLS syndrome...
January 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28050599/optic-atrophy-cataracts-lipodystrophy-lipoatrophy-and-peripheral-neuropathy-caused-by-a-de-novo-opa3-mutation
#20
Stephanie C Bourne, Katelin N Townsend, Casper Shyr, Allison Matthews, Scott A Lear, Raj Attariwala, Anna Lehman, Wyeth W Wasserman, Clara van Karnebeek, Graham Sinclair, Hilary Vallance, William T Gibson
We describe a woman who presented with cataracts, optic atrophy, lipodystrophy/lipoatrophy, and peripheral neuropathy. Exome sequencing identified a c.235C > G p.(Leu79Val) variant in the optic atrophy 3 (OPA3) gene that was confirmed to be de novo. This report expands the severity of the phenotypic spectrum of autosomal dominant OPA3 mutations.
January 2017: Cold Spring Harbor Molecular Case Studies
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