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Cold Spring Harbor Molecular Case Studies

Tilmann Bochtler, Stefan Fröhling, Wilko Weichert, Volker Endris, Christian Thiede, Barbara Hutter, Michael Hundemer, Anthony D Ho, Alwin Krämer
Here, we report the case of an acute promyelocytic leukemia (APL) patient who-although negative for FLT3 mutations at diagnosis-developed isolated FLT3 tyrosine kinase II domain (FLT3-TKD)-positive meningeal relapse, which, in retrospect, could be traced back to a minute bone marrow subclone present at first diagnosis. Initially, the 48-yr-old female diagnosed with high-risk APL had achieved complete molecular remission after standard treatment with all-trans retinoic acid (ATRA) and chemotherapy according to the AIDA (ATRA plus idarubicin) protocol...
September 2016: Cold Spring Harbor Molecular Case Studies
Frank Y Lin, Katie Bergstrom, Richard Person, Abhishek Bavle, Leomar Y Ballester, Sarah Scollon, Robin Raesz-Martinez, Andrew Jea, Sherri Birchansky, David A Wheeler, Stacey L Berg, Murali M Chintagumpala, Adekunle M Adesina, Christine Eng, Angshumoy Roy, Sharon E Plon, D Williams Parsons
The integration of genome-scale studies such as whole-exome sequencing (WES) into the clinical care of children with cancer has the potential to provide insight into the genetic basis of an individual's cancer with implications for clinical management. This report describes the results of clinical tumor and germline WES for a patient with a rare tumor diagnosis, rosette-forming glioneuronal tumor of the fourth ventricle (RGNT). Three pathogenic gene alterations with implications for clinical care were identified: somatic activating hotspot mutations in FGFR1 (p...
September 2016: Cold Spring Harbor Molecular Case Studies
Kyaw L Aung, Tracy L Stockley, Stefano Serra, Suzanne Kamel-Reid, Philippe L Bedard, Lillian L Siu
Recent advances in molecular profiling technologies allow genetic driver events in individual tumors to be identified. The hypothesis behind this ongoing molecular profiling effort is that improvement in patients' clinical outcomes will be achieved by inhibiting these discovered genetic driver events with matched targeted drugs. This hypothesis is currently being tested in oncology clinics with variable early results. Herein, we present our experience with a case of advanced colorectal cancer (CRC) with an ERBB2 p...
September 2016: Cold Spring Harbor Molecular Case Studies
Niklas Smedemark-Margulies, Catherine A Brownstein, Sigella Vargas, Sahil K Tembulkar, Meghan C Towne, Jiahai Shi, Elisa Gonzalez-Cuevas, Kevin X Liu, Kaya Bilguvar, Robin J Kleiman, Min-Joon Han, Alcy Torres, Gerard T Berry, Timothy W Yu, Alan H Beggs, Pankaj B Agrawal, Joseph Gonzalez-Heydrich
We describe a child with onset of command auditory hallucinations and behavioral regression at 6 yr of age in the context of longer standing selective mutism, aggression, and mild motor delays. His genetic evaluation included chromosomal microarray analysis and whole-exome sequencing. Sequencing revealed a previously unreported heterozygous de novo mutation c.385G>A in ATP1A3, predicted to result in a p.V129M amino acid change. This gene codes for a neuron-specific isoform of the catalytic α-subunit of the ATP-dependent transmembrane sodium-potassium pump...
September 2016: Cold Spring Harbor Molecular Case Studies
Kenneth S Chen, Woo Sun Kwon, Jiwoong Kim, Su Jin Heo, Hyo Song Kim, Hyo Ki Kim, Soo Hee Kim, Won Suk Lee, Hyun Cheol Chung, Sun Young Rha, Tae Hyun Hwang
Osteosarcoma is the most common primary bone cancer. It can be cured by aggressive surgery and chemotherapy, but outcomes for metastatic or chemoresistant disease remain dismal. Cancer sequencing studies have shown that the p53 pathway is dysregulated in nearly every case, often by translocation; however, no studies of osteosarcoma evolution or intratumor heterogeneity have been done to date. We studied a patient with chemoresistant, metastatic disease over the course of 3 years. We performed exome sequencing on germline DNA and DNA collected from tumor at three separate time points...
September 2016: Cold Spring Harbor Molecular Case Studies
Abby M Moskowitz, Newell Belnap, Ashley L Siniard, Szabolcs Szelinger, Ana M Claasen, Ryan F Richholt, Matt De Both, Jason J Corneveaux, Chris Balak, Ignazio S Piras, Megan Russell, Amanda L Courtright, Sampath Rangasamy, Keri Ramsey, David W Craig, Vinodh Narayanan, Matt J Huentelman, Isabelle Schrauwen
Recently, mutations in the zinc finger MYND-type containing 11 (ZMYND11) gene were identified in patients with autism spectrum disorders, intellectual disability, aggression, and complex neuropsychiatric features, supporting that this gene is implicated in 10p15.3 microdeletion syndrome. We report a novel de novo variant in the ZMYND11 gene (p.Ser421Asn) in a patient with a complex neurodevelopmental phenotype. The patient is a 24-yr-old Caucasian/Filipino female with seizures, global developmental delay, sensorineural hearing loss, hypotonia, dysmorphic features, and other features including a happy disposition and ataxic gait similar to Angelman syndrome...
September 2016: Cold Spring Harbor Molecular Case Studies
Sarah B Pierce, Suleyman Gulsuner, Gail A Stapleton, Tom Walsh, Ming K Lee, Jessica B Mandell, Augusto Morales, Rachel E Klevit, Mary-Claire King, R Curtis Rogers
Mutations in nuclear genes required for the replication and maintenance of mitochondrial DNA cause progressive multisystemic neuromuscular disorders with overlapping phenotypes. Biallelic mutations in C10orf2, encoding the Twinkle mitochondrial DNA helicase, lead to infantile-onset cerebellar ataxia (IOSCA), as well as milder and more severe phenotypes. We present a 13-year-old girl with ataxia, severe hearing loss, optic atrophy, peripheral neuropathy, and hypergonadotropic hypogonadism. Whole-exome sequencing revealed that the patient is compound heterozygous for previously unreported variants in the C10orf2 gene: a paternally inherited frameshift variant (c...
July 2016: Cold Spring Harbor Molecular Case Studies
Laurie Beth Griffin, Frances A Farley, Anthony Antonellis, Catherine E Keegan
Mutations in FGD1 cause Aarskog-Scott syndrome (AAS), an X-linked condition characterized by abnormal facial, skeletal, and genital development due to abnormal embryonic morphogenesis and skeletal formation. Here we report a novel FGD1 mutation in a family with atypical features of AAS, specifically bilateral upper and lower limb congenital joint contractures and cardiac abnormalities. The male proband and his affected maternal uncle are hemizygous for the novel FGD1 mutation p.Arg921X. This variant is the most carboxy-terminal FGD1 mutation identified in a family with AAS and is predicted to truncate the FGD1 protein at the second to last amino acid of the carboxy-terminal pleckstrin homology (PH) domain...
July 2016: Cold Spring Harbor Molecular Case Studies
Teresa W-M Fan, Marc O Warmoes, Qiushi Sun, Huan Song, Jadwiga Turchan-Cholewo, Jeremiah T Martin, Angela Mahan, Richard M Higashi, Andrew N Lane
Cancer and stromal cell metabolism is important for understanding tumor development, which highly depends on the tumor microenvironment (TME). Cell or animal models cannot recapitulate the human TME. We have developed an ex vivo paired cancerous (CA) and noncancerous (NC) human lung tissue approach to explore cancer and stromal cell metabolism in the native human TME. This approach enabled full control of experimental parameters and acquisition of individual patient's target tissue response to therapeutic agents while eliminating interferences from genetic and physiological variations...
July 2016: Cold Spring Harbor Molecular Case Studies
Jessica N Lacy, Jacob C Ulirsch, Rachael F Grace, Meghan C Towne, John Hale, Narla Mohandas, Samuel E Lux, Pankaj B Agrawal, Vijay G Sankaran
Whole-exome sequencing is increasingly used for diagnosis and identification of appropriate therapies in patients. Here, we present the case of a 3-yr-old male with a lifelong and severe transfusion-dependent anemia of unclear etiology, despite an extensive clinical workup. Given the difficulty of making the diagnosis and the potential side effects from performing interventions in patients with a congenital anemia of unknown etiology, we opted to perform whole-exome sequencing on the patient and his parents...
July 2016: Cold Spring Harbor Molecular Case Studies
Eva Leinøe, Ove Juul Nielsen, Lars Jønson, Maria Rossing
The increasing availability of genome-wide analysis has made it possible to rapidly sequence the exome of patients with undiagnosed or unresolved medical conditions. Here, we present the case of a 64-yr-old male patient with schistocytes in the peripheral blood smear and a complex and life-threatening coagulation disorder causing recurrent venous thromboembolic events, severe thrombocytopenia, and subdural hematomas. Whole-exome sequencing revealed a frameshift mutation (C3AR1 c.355-356dup, p.Asp119Alafs*19) resulting in a premature stop codon in C3AR1 (Complement Component 3a Receptor 1)...
July 2016: Cold Spring Harbor Molecular Case Studies
Marni J Falk, Lishuang Shen, Xiaowu Gai
No abstract text is available yet for this article.
May 2016: Cold Spring Harbor Molecular Case Studies
Hung-Chun Yu, Curtis R Coughlin, Elizabeth A Geiger, Blake J Salvador, Ellen R Elias, Jean L Cavanaugh, Kathryn C Chatfield, Shelley D Miyamoto, Tamim H Shaikh
Restrictive cardiomyopathy (RCM) is a rare cause of heart muscle disease with the highest mortality rate among cardiomyopathy types. The etiology of RCM is poorly understood, although genetic causes have been implicated, and syndromic associations have been described. Here, we describe a patient with an atrial septal defect and restrictive cardiomyopathy along with craniofacial anomalies and intellectual disabilities. Initial screening using chromosomal microarray analysis (CMA) identified a maternally inherited 2q13 microdeletion...
May 2016: Cold Spring Harbor Molecular Case Studies
Mugdha Joshi, Irina Anselm, Jiahai Shi, Tejus A Bale, Meghan Towne, Klaus Schmitz-Abe, Laura Crowley, Felix C Giani, Shideh Kazerounian, Kyriacos Markianos, Hart G Lidov, Rebecca Folkerth, Vijay G Sankaran, Pankaj B Agrawal
We describe a large Lebanese family with two affected members, a young female proband and her male cousin, who had multisystem involvement including profound global developmental delay, severe hypotonia and weakness, respiratory insufficiency, blindness, and lactic acidemia-findings consistent with an underlying mitochondrial disorder. Whole-exome sequencing was performed on DNA from the proband and both parents. The proband and her cousin carried compound heterozygous mutations in the PMPCA gene that encodes for α-mitochondrial processing peptidase (α-MPP), a protein likely involved in the processing of mitochondrial proteins...
May 2016: Cold Spring Harbor Molecular Case Studies
G Steven Bova, Heini M L Kallio, Matti Annala, Kati Kivinummi, Gunilla Högnäs, Sergei Häyrynen, Tommi Rantapero, Virpi Kivinen, William B Isaacs, Teemu Tolonen, Matti Nykter, Tapio Visakorpi
We report the first combined analysis of whole-genome sequence, detailed clinical history, and transcriptome sequence of multiple prostate cancer metastases in a single patient (A21). Whole-genome and transcriptome sequence was obtained from nine anatomically separate metastases, and targeted DNA sequencing was performed in cancerous and noncancerous foci within the primary tumor specimen removed 5 yr before death. Transcriptome analysis revealed increased expression of androgen receptor (AR)-regulated genes in liver metastases that harbored an AR p...
May 2016: Cold Spring Harbor Molecular Case Studies
Swati Gupta, Somayyeh Fahiminiya, Tracy Wang, Laura Dempsey Nunez, David S Rosenblatt, William T Gibson, Brian Gilfix, John J M Bergeron, Loydie A Jerome-Majewska
Using whole-exome sequencing, we identified homozygous mutations in two unlinked genes, SEC23A c.1200G>C (p.M400I) and MAN1B1 c.1000C>T (p.R334C), associated with congenital birth defects in two patients from a consanguineous family. Patients presented with carbohydrate-deficient transferrin, tall stature, obesity, macrocephaly, and maloccluded teeth. The parents were healthy heterozygous carriers for both mutations and an unaffected sibling with tall stature carried the heterozygous mutation in SEC23A only...
May 2016: Cold Spring Harbor Molecular Case Studies
Elaine R Mardis
No abstract text is available yet for this article.
March 2016: Cold Spring Harbor Molecular Case Studies
Katayoon Kasaian, Sam M Wiseman, Blair A Walker, Jacqueline E Schein, Martin Hirst, Richard A Moore, Andrew J Mungall, Marco A Marra, Steven J M Jones
Medullary thyroid cancer (MTC) is a malignancy of the calcitonin-producing parafollicular cells of the thyroid gland. Surgery is the only curative treatment for this cancer. External beam radiation therapy is reserved for adjuvant treatment of MTC with aggressive features. Targeted therapeutics vandetanib and cabozantinib are approved for the treatment of aggressive and metastatic tumors that are not amenable to surgery. The use of these multikinase inhibitors are supported by the observed overactivation of the RET oncoprotein in a large subpopulation of MTCs...
March 2016: Cold Spring Harbor Molecular Case Studies
Ayşegül Ozantürk, Erica E Davis, Aniko Sabo, Marjan M Weiss, Donna Muzny, Shannon Dugan-Perez, Erik A Sistermans, Richard A Gibbs, Köksal R Özgül, Dilek Yalnızoglu, Esra Serdaroglu, Ali Dursun, Nicholas Katsanis
Genetic studies grounded on monogenic paradigms have accelerated both gene discovery and molecular diagnosis. At the same time, complex genomic rearrangements are also appreciated as potent drivers of disease pathology. Here, we report two male siblings with a dysmorphic face, ambiguous genitalia, intellectual disability, and speech delay. Through quad-based whole-exome sequencing and concomitant molecular cytogenetic testing, we identified two copy-number variants (CNVs) in both affected individuals likely arising from a balanced translocation: a 13...
March 2016: Cold Spring Harbor Molecular Case Studies
Jeremy D K Parker, Yaoqing Shen, Erin Pleasance, Yvonne Li, Jacqueline E Schein, Yongjun Zhao, Richard Moore, Joanna Wegrzyn-Woltosz, Kerry J Savage, Andrew P Weng, Randy D Gascoyne, Steven Jones, Marco Marra, Janessa Laskin, Aly Karsan
In an attempt to assess potential treatment options, whole-genome and transcriptome sequencing were performed on a patient with an unclassifiable small lymphoproliferative disorder. Variants from genome sequencing were prioritized using a combination of comparative variant distributions in a spectrum of lymphomas, and meta-analyses of gene expression profiling. In this patient, the molecular variants that we believe to be most relevant to the disease presentation most strongly resemble a diffuse large B-cell lymphoma (DLBCL), whereas the gene expression data are most consistent with a low-grade chronic lymphocytic leukemia (CLL)...
March 2016: Cold Spring Harbor Molecular Case Studies
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