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Cold Spring Harbor Molecular Case Studies

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https://www.readbyqxmd.com/read/30087100/surgical-and-molecular-characterization-of-primary-and-metastatic-disease-in-a-neuroendocrine-tumor-arising-in-a-tailgut-cyst
#1
Jennifer Erdrich, Kurt Schaberg, Michael S Khodadoust, Li Zhou, Andrew A Shelton, Brendan C Visser, James M Ford, Ashara A Alizadeh, Stephen R Quake, Pamela L Kunz, John F Beausang
Neuroendocrine tumors arising from tailgut cysts are rare but increasingly reported entity with gene expression profiles that may be indicative of the gastrointestinal cell of origin. We present a case report describing the unique pathological and genomic characteristics of a tailgut cyst neuroendocrine tumor that metastasized to liver. The histologic and immunohistochemical findings were consistent with a well-differentiated neuroendocrine tumor. Genomic testing indicates a germline frame-shift in BRCA1 and a few somatic mutations of unknown significance...
August 7, 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/30054298/inframe-de-novo-mutation-in-bicd2-in-two-patients-with-muscular-atrophy-and-arthrogryposis
#2
Daniel C Koboldt, Rama Kastury, Megan A Waldrop, Benjamin J Kelly, Theresa Mihalic Mosher, Heather McLaughlin, Don Corsmeier, Jonathan L Slaughter, Kevin M Flanigan, Kim L McBride, Lakshmi Mehta, Richard K Wilson, Peter White
We describe two unrelated patients, a 12-year-old female and a 6-year-old male, with congenital contractures and severe congenital muscular atrophy. Exome and genome sequencing of the probands and their unaffected parents revealed that they have the same de novo deletion in BICD2 (c.1636_1638delAAT). The variant, which has never been reported, results in an inframe 3 base pair deletion and is predicted to cause loss of an evolutionarily conserved Asparagine residue at position 546 in the protein. Missense mutations in BICD2 cause autosomal dominant spinal muscular atrophy, lower-extremity predominant 2 (SMALED2), a disease characterized by muscle weakness and arthrogryposis of early onset and slow progression...
July 27, 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/30026388/exome-sequencing-of-an-adolescent-with-nonalcoholic-fatty-liver-disease-identifies-a-clinically-actionable-case-of-wilson-disease
#3
Julia Wattacheril, Patrick R Shea, Saeed Mohammad, Cynthia Behling, Vimla Aggarwal, Laura A Wilson, Katherine P Yates, Joy Ito, Mark Fishbein, Nicholas Stong, Joel E Lavine, David B Goldstein
Diagnostic whole exome sequencing has proven highly successful in a range of rare diseases, particularly early onset genetic conditions. In more common conditions, however, exome sequencing for diagnostic purposes remains the exception. Here we describe a patient initially diagnosed with a common, complex liver disease, nonalcoholic fatty liver disease (NAFLD), who was determined to have Wilson Disease (WD) upon research-related exome sequencing. The patient presented as a 14.5-year-old adolescent with chronically elevated aminotransferases, normal ceruloplasmin, and histologic examination consistent with NAFLD with advanced fibrosis...
July 19, 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29970384/further-evidence-for-the-involvement-of-efl1-in-a-shwachman-diamond-like-syndrome-and-expansion-of-the-phenotypic-features
#4
Queenie K-G Tan, Heidi Cope, Rebecca C Spillmann, Nicholas Stong, Yong-Hui Jiang, Marie T McDonald, Jennifer A Rothman, Megan W Butler, Donald P Frush, Ralph S Lachman, Brendan Lee, Carlos A Bacino, Melanie J Bonner, Chad M McCall, Avani A Pendse, Nicole Walley, Udn Members, Vandana Shashi, Loren D M Pena
Recent evidence has implicated EFL1 in a phenotype overlapping Shwachman-Diamond syndrome (SDS), with the functional interplay between EFL1 and the previously known causative gene SBDS accounting for the similarity in clinical features. Relatively little is known about the phenotypes associated with pathogenic variants in the EFL1 gene, but the initial indication was that phenotypes may be more severe, when compared with SDS. We report a pediatric patient who presented with a metaphyseal dysplasia and was found to have biallelic variants in EFL1 on reanalysis of trio whole exome sequencing data...
July 3, 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29945942/reclassification-of-the-braf-p-ile208val-variant-by-case-level-data-sharing
#5
Andrew R Grant, Sarah E Hemphill, Lisa M Vincent, Heidi L Rehm
The ClinVar database is a useful tool for patients and physicians to view variant interpretations submitted by clinical and non-clinical labs. However, variants of uncertain significance (VUS) in ClinVar can pose a significant burden on patients. If possible, it is important to resolve discrepancies and uncertainties surrounding interpreted variants. Here we highlight a case of a family who received a report of a variant (c.622A>G, p.Ile208Val) in BRAF following prenatal RASopathy testing. The variant had been previously classified by our laboratory as a VUS, so the mother contacted our lab via ClinVar for further information which prompted re-evaluation of the variant...
June 26, 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/30068734/corrigendum-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
#6
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
No abstract text is available yet for this article.
August 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/30068733/endometrial-cancer-with-an-eml4-alk-rearrangement
#7
Jeffrey W Craig, Bradley J Quade, Michael G Muto, Laura E MacConaill
An 85-yr-old woman was diagnosed with endometrial adenocarcinoma, endometrioid type. Imaging studies showed a large tumor distending the endometrial canal without evidence of local invasion or extrauterine disease. A hysterectomy was performed, followed by microscopic examination of longitudinal tissue sections. Histopathological review showed only focal myometrial invasion, equivocal lymphovascular invasion, and negative bilateral sentinel lymph nodes (FIGO stage IA). A sample of the tumor was submitted for molecular testing (massively parallel sequencing on OncoPanel) and was found to harbor an inversion on Chromosome 2 resulting in an EML4-ALK gene fusion...
August 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/30068732/germline-sdha-mutations-in-children-and-adults-with-cancer
#8
Marianne Dubard Gault, Diana Mandelker, Deborah DeLair, Carolyn R Stewart, Yelena Kemel, Margaret R Sheehan, Beth Siegel, Jennifer Kennedy, Vanessa Marcell, Angela Arnold, Hikmat Al-Ahmadie, Shakeel Modak, Mark Robson, Neerav Shukla, Stephen Roberts, Joseph Vijai, Sabine Topka, Alex Kentsis, Karen Cadoo, Maria Carlo, Alicia Latham Schwark, Ed Reznik, Renzo Dinatale, Jaclyn Hechtman, Ester Borras Flores, Sowmaya Jairam, Ciyu Yang, Yirong Li, Erol Can Bayraktar, Ozge Ceyhan-Birsoy, Liying Zhang, Wendy Kohlman, Joshua Schiffman, Zsofia Stadler, Kivanc Birsoy, Andrew Kung, Kenneth Offit, Michael F Walsh
Mutations in succinate dehydrogenase complex genes predispose to familial paraganglioma-pheochromocytoma syndrome (FPG) and gastrointestinal stromal tumors (GIST). Here we describe cancer patients undergoing agnostic germline testing at Memorial Sloan Kettering Cancer Center and found to harbor germline SDHA mutations. Using targeted sequencing covering the cancer census genes, we identified 10 patients with SDHA germline mutations. Cancer diagnoses for these patients carrying SDHA germline mutations included neuroblastoma ( n = 1), breast ( n = 1), colon ( n = 1), renal ( n = 1), melanoma and uterine ( n = 1), prostate ( n = 1), endometrial ( n = 1), bladder ( n = 1), and gastrointestinal stromal tumor (GIST) ( n = 2)...
August 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29907598/clinical-response-of-the-novel-activating-alk-i1171t-mutation-in-neuroblastoma-to-the-alk-inhibitor-ceritinib
#9
Jikui Guan, Susanne Fransson, Joachim Tetteh Siaw, Diana Treis, Jimmy Van den Eynden, Damini Chand, Ganesh Umapathy, Kristina Ruuth, Petter Svenberg, Sandra Wessman, Alia Shamikh, Hans Jacobsson, Lena Gordon, Jakob Stenman, Pär-Johan Svensson, Magnus Hansson, Erik Larsson, Tommy Martinsson, Ruth H Palmer, Per Kogner, Bengt Hallberg
Tumors with anaplastic lymphoma kinase (ALK) fusion rearrangements, including non-small-cell lung cancer and anaplastic large cell lymphoma, are highly sensitive to ALK tyrosine kinase inhibitors (TKIs), underscoring the notion that such cancers are addicted to ALK activity. Although mutations in ALK are heavily implicated in childhood neuroblastoma, response to the ALK TKI crizotinib has been disappointing. Embryonal tumors in patients with DNA repair defects such as Fanconi anemia (FA) often have a poor prognosis, because of lack of therapeutic options...
August 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29903892/de-novo-myh9-mutation-in-congenital-scalp-hemangioma
#10
Elena I Fomchenko, Daniel Duran, Sheng Chih Jin, Weilai Dong, E Zeynep Erson-Omay, Prince Antwi, August Allocco, Jonathan R Gaillard, Anita Huttner, Murat Gunel, Michael L DiLuna, Kristopher T Kahle
Congenital hemangiomas are tumor-like vascular malformations with poorly understood pathogenesis. We report the case of a neonate with a massive congenital scalp hemangioma that required urgent neurosurgical removal on the second day of life because of concern for high-flow arteriovenous shunting. Exome sequencing identified a rare damaging de novo germline mutation in MYH9 (c.5308C>T, p.[Arg1770Cys]), encoding the MYH9 nonmuscle myosin IIA. MYH9 has a probability of loss-of-function intolerance (pLI) score of >0...
August 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29848554/extremely-hypomorphic-and-severe-deep-intronic-variants-in-the-abca4-locus-result-in-varying-stargardt-disease-phenotypes
#11
Jana Zernant, Winston Lee, Takayuki Nagasaki, Frederick T Collison, Gerald A Fishman, Mette Bertelsen, Thomas Rosenberg, Peter Gouras, Stephen H Tsang, Rando Allikmets
Autosomal recessive Stargardt disease (STGD1, MIM 248200) is caused by mutations in the ABCA4 gene. Complete sequencing of the ABCA4 locus in STGD1 patients identifies two expected disease-causing alleles in ∼75% of patients and only one mutation in ∼15% of patients. Recently, many possibly pathogenic variants in deep intronic sequences of ABCA4 have been identified in the latter group. We extended our analyses of deep intronic ABCA4 variants and determined that one of these, c.4253+43G>A (rs61754045), is present in 29/1155 (2...
August 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29802153/co-occurrence-of-a-maternally-inherited-dnmt3a-duplication-and-a-paternally-inherited-pathogenic-variant-in-ezh2-in-a-child-with-growth-retardation-and-severe-short-stature-atypical-weaver-syndrome-or-evidence-of-a-dnmt3a-dosage-effect
#12
Katarzyna Polonis, Patrick R Blackburn, Raul A Urrutia, Gwen A Lomberk, Teresa Kruisselbrink, Margot A Cousin, Nicole J Boczek, Nicole L Hoppman, Dusica Babovic-Vuksanovic, Eric W Klee, Pavel N Pichurin
Overgrowth syndromes are a clinically heterogeneous group of disorders characterized by localized or generalized tissue overgrowth and varying degrees of developmental and intellectual disability. An expanding list of genes associated with overgrowth syndromes include the histone methyltransferase genes EZH2 and NSD1 , which cause Weaver and Sotos syndrome, respectively, and the DNA methyltransferase ( DNMT3A ) gene that results in Tatton-Brown-Rahman syndrome (TBRS). Here, we describe a 5-year-old female with a paternally inherited pathogenic mutation in EZH2 (c...
August 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29798843/a-novel-de-novo-cdh1-germline-variant-aids-in-the-classification-of-carboxy-terminal-e-cadherin-alterations-predicted-to-escape-nonsense-mediated-mrna-decay
#13
Kate Krempely, Rachid Karam
Most truncating cadherin 1 ( CDH1 ) pathogenic alterations confer an elevated lifetime risk of diffuse gastric cancer (DGC) and lobular breast cancer (LBC). However, transcripts containing carboxy-terminal premature stop codons have been demonstrated to escape the nonsense-mediated mRNA decay pathway, and gastric and breast cancer risks associated with these truncations should be carefully evaluated. A female patient underwent multigene panel testing because of a personal history of invasive LBC diagnosed at age 54, which identified the germline CDH1 nonsense alteration, c...
August 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29728376/reconciling-newborn-screening-and-a-novel-splice-variant-in-btd-associated-with-partial-biotinidase-deficiency-a-babyseq-project-case-report
#14
Jaclyn B Murry, Kalotina Machini, Ozge Ceyhan-Birsoy, Amy Kritzer, Joel B Krier, Matthew S Lebo, Shawn Fayer, Casie A Genetti, Grace E VanNoy, Timothy W Yu, Pankaj B Agrawal, Richard B Parad, Ingrid A Holm, Amy L McGuire, Robert C Green, Alan H Beggs, Heidi L Rehm
Here, we report a newborn female infant from the well-baby cohort of the BabySeq Project who was identified with compound heterozygous BTD gene variants. The two identified variants included a well-established pathogenic variant (c.1612C>T, p.Arg538Cys) that causes profound biotinidase deficiency (BTD) in homozygosity. In addition, a novel splice variant (c.44+1G>A, p.?) was identified in the invariant splice donor region of intron 1, potentially predictive of loss of function. The novel variant was predicted to impact splicing of exon 1; however, given the absence of any reported pathogenic variants in exon 1 and the presence of alternative splicing with exon 1 absent in most tissues in the GTEx database, we assigned an initial classification of uncertain significance...
August 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29895553/9p24-triplication-and-15q13-deletion-in-syndromic-hydrocephalus-with-diffuse-villous-hyperplasia-of-the-choroid-plexus
#15
Charuta Furey, Prince Antwi, Daniel Duran, Andrew T Timberlake, Carol Nelson-Williams, Charles C Matouk, Michael L DiLuna, Murat Günel, Kristopher T Kahle
Hydrocephalus, a disorder of impaired cerebrospinal fluid (CSF) homeostasis, often results from an imbalance between CSF production and reabsorption. Rarely, hydrocephalus is the consequence of CSF hypersecretion in the context of diffuse villous hyperplasia of the choroid plexus (DVHCP). The limited genetic information in previously reported cases suggests a high prevalence of gains of chromosome 9p in this disease, although the critical genes involved in DVHCP pathogenesis have not been identified. Here, we report a patient with syndromic hydrocephalus with DVHCP associated with a novel 9p24...
June 12, 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29891567/clonal-dynamics-of-donor-derived-mds-after-unrelated-hct-for-high-risk-pediatric-b-lymphoblastic-leukemia
#16
Jason R Schwartz, Michael P Walsh, Jing Ma, Tamara Lamprecht, Shuoguo Wang, Gang Wu, Susana Raimondi, Brandon Triplett, Jeffery Klco
Donor-derived hematologic malignancies are rare complications of hematopoietic cell transplantation (HCT). Although these are commonly either a myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML), in general, they are a heterogeneous group of diseases and a unified mechanism for their development has remained elusive. Here we report next generation sequencing, including whole exome sequencing (WES), whole genome sequencing (WGS), and targeted sequencing, of a case of donor-derived MDS (dMDS) following HCT for high-risk B-lymphoblastic leukemia (B-ALL) in an adolescent...
June 11, 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29858379/erratum-whole-exome-sequencing-identifies-germline-mutation-in-tp53-and-atrx-in-a-child-with-genomically-aberrant-at-rt-and-her-mother-with-anaplastic-astrocytoma
#17
Kristiina Nordfors, Joonas Haapasalo, Ebrahim Afyounian, Joonas Tuominen, Matti Annala, Sergei Häyrynen, Ritva Karhu, Pauli Helén, Olli Lohi, Matti Nykter, Hannu Haapasalo, Kirsi J Granberg
No abstract text is available yet for this article.
June 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29858378/17p13-3-quadruplication-a-prenatal-and-postpartum-clinical-characterization-of-a-copy-number-variant
#18
Nicholas Farris, Helena Wu, Sara Said-Delgado, Barrie Suskin, Susan Klugman
Prenatal genetic testing has advanced rapidly in the past decade. However, not all results, including variants, are well understood. We report the finding of a 2.5-Mb gene region quadruplication of Chromosome 17p13.3. This region is well characterized for the deletion leading to Miller-Dieker syndrome but has an unclear replication phenotype. Invasive testing performed after ultrasound abnormalities were seen revealed the quadruplication sequence as well as a short segment (850 kb) with x5 copy number variation...
June 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29695406/a-novel-association-of-campomelic-dysplasia-and-hydrocephalus-with-an-unbalanced-chromosomal-translocation-upstream-of-sox9
#19
Prince Antwi, Christopher S Hong, Daniel Duran, Sheng Chih Jin, Weilai Dong, Michael DiLuna, Kristopher T Kahle
Campomelic dysplasia is a rare skeletal dysplasia characterized by Pierre Robin sequence, craniofacial dysmorphism, shortening and angulation of long bones, tracheobronchomalacia, and occasionally sex reversal. The disease is due to mutations in SOX9 or chromosomal rearrangements involving the long arm of Chromosome 17 harboring the SOX9 locus. SOX9, a transcription factor, is indispensible in establishing and maintaining neural stem cells in the central nervous system. We present a patient with angulation of long bones and external female genitalia on prenatal ultrasound who was subsequently found to harbor the chromosomal abnormality 46, XY, t(6;17) (p21...
June 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29549119/the-case-for-early-use-of-rapid-whole-genome-sequencing-in-management-of-critically-ill-infants-late-diagnosis-of-coffin-siris-syndrome-in-an-infant-with-left-congenital-diaphragmatic-hernia-congenital-heart-disease-and-recurrent-infections
#20
Nathaly M Sweeney, Shareef A Nahas, Shimul Chowdhury, Miguel Del Campo, Marilyn C Jones, David P Dimmock, Stephen F Kingsmore
Congenital diaphragmatic hernia (CDH) results from incomplete formation of the diaphragm leading to herniation of abdominal organs into the thoracic cavity. CDH is associated with pulmonary hypoplasia, congenital heart disease, and pulmonary hypertension. Genetically, it is associated with aneuploidies, chromosomal copy-number variants, and single gene mutations. CDH is the most expensive noncardiac congenital defect. Management frequently requires implementation of extracorporeal membrane oxygenation (ECMO), which increases management expenditures 2...
June 2018: Cold Spring Harbor Molecular Case Studies
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