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Clinical molecular genetics

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https://www.readbyqxmd.com/read/28453651/a-panoromic-view-of-personal-cancer-genomes
#1
Lidia Mateo, Oriol Guitart-Pla, Carles Pons, Miquel Duran-Frigola, Roberto Mosca, Patrick Aloy
The massive molecular profiling of thousands of cancer patients has led to the identification of many tumor type specific driver genes. However, only a few (or none) of them are present in each individual tumor and, to enable precision oncology, we need to interpret the alterations found in a single patient. Cancer PanorOmics (http://panoromics.irbbarcelona.org) is a web-based resource to contextualize genomic variations detected in a personal cancer genome within the body of clinical and scientific evidence available for 26 tumor types, offering complementary cohort- and patient-centric views...
April 27, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28453600/whole-exome-sequencing-in-eight-thai-patients-with-leber-congenital-amaurosis-reveals-mutations-in-the-ctnna1-and-cyp4v2-genes
#2
Worapoj Jinda, Todd D Taylor, Yutaka Suzuki, Wanna Thongnoppakhun, Chanin Limwongse, Patcharee Lertrit, Adisak Trinavarat, La-Ongsri Atchaneeyasakul
Purpose: Our goal was to describe the clinical and molecular genetic findings in Thai patients with Leber congenital amaurosis (LCA). Methods: Whole exome sequencing (WES) was performed in eight unrelated patients. All genes responsible for inherited retinal diseases (IRDs) based on RetNet were selected for analysis. Potentially causative variants were filtered through a bioinformatics pipeline and validated using Sanger sequencing. Segregation analysis of the causative genes was performed in family members when available...
April 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28453505/breast-cancer-intra-tumor-heterogeneity-one-tumor-different-entities
#3
José Esparza-López, Elizabet Escobar-Arriaga, Santos Soto-Germes, María de Jesús Ibarra-Sánchez
In recent years, it has become evident that intra-tumor heterogeneity of breast cancer is a big challenge for the diagnosis, treatment, and clinical course of tumor-bearing patients. The advances in molecular biology and other technologies have led to the knowledge that a breast cancer tumor is comprised of multiple cellular entities. Here we review the two theories that have been described, trying to explain the origin of intra-tumor heterogeneity: clonal evolution and cancer stem cells. The first one considers that a single cell gives rise to many subpopulations through the accumulation of multiple aberrations, while the cancer stem cells theory foresees a hierarchical tumor evolution where only a few cells with self-renewal capacity give rise to different subpopulations...
March 2017: Revista de Investigación Clínica; Organo del Hospital de Enfermedades de la Nutrición
https://www.readbyqxmd.com/read/28449065/a-homozygous-missense-mutation-in-eral1-encoding-a-mitochondrial-rrna-chaperone-causes-perrault-syndrome
#4
Iliana A Chatzispyrou, Marielle Alders, Sergio Guerrero-Castillo, Ruben Zapata Perez, Martin A Haagmans, Laurent Mouchiroud, Janet Koster, Rob Ofman, Frank Baas, Hans R Waterham, Johannes N Spelbrink, Johan Auwerx, Marcel M Mannens, Riekelt H Houtkooper, Astrid S Plomp
Perrault syndrome (PS) is a rare recessive disorder characterized by ovarian dysgenesis and sensorineural deafness. It is clinically and genetically heterogeneous, and previously mutations have been described in different genes, mostly related to mitochondrial proteostasis. We diagnosed three unrelated females with PS and set out to identify the underlying genetic cause using exome sequencing. We excluded mutations in the known PS genes, but identified a single homozygous mutation in the ERAL1 gene (c.707A>T; p...
April 25, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28448960/utility-of-genomic-analysis-in-differentiating-synchronous-and-metachronous-lung-adenocarcinomas-from-primary-adenocarcinomas-with-intrapulmonary-metastasis
#5
Jad Saab, Hamid Zia, Susan Mathew, Michael Kluk, Navneet Narula, Helen Fernandes
Distinguishing synchronous and metachronous primary lung adenocarcinomas from adenocarcinomas with intrapulmonary metastasis is essential for optimal patient management. In this study, multiple lung adenocarcinomas occurring in the same patient were evaluated using comprehensive histopathologic evaluation supplemented with molecular analysis. The cohort included 18 patients with a total of 52 lung adenocarcinomas. Eleven patients had a new diagnosis of multiple adenocarcinomas in the same lobe (n=5) or different lobe (n=6)...
April 24, 2017: Translational Oncology
https://www.readbyqxmd.com/read/28448599/simulation-of-the-dynamics-of-primary-immunodeficiencies-in-cd4-t-cells
#6
Gabriel N Teku, Mauno Vihinen
Primary immunodeficiencies (PIDs) form a large and heterogeneous group of mainly rare disorders that affect the immune system. T-cell deficiencies account for about one-tenth of PIDs, most of them being monogenic. Apart from genetic and clinical information, lots of other data are available for PID proteins and genes, including functions and interactions. Thus, it is possible to perform systems biology studies on the effects of PIDs on T-cell physiology and response. To achieve this, we reconstructed a T-cell network model based on literature mining and TPPIN, a previously published core T-cell network, and performed semi-quantitative dynamic network simulations on both normal and T-cell PID failure modes...
2017: PloS One
https://www.readbyqxmd.com/read/28448556/a-highly-specific-and-sensitive-massive-parallel-sequencer-based-test-for-somatic-mutations-in-non-small-cell-lung-cancer
#7
Yoshiaki Inoue, Jun Shiihara, Hitoshi Miyazawa, Hiromitsu Ohta, Megumi Higo, Yoshiaki Nagai, Kunihiko Kobayashi, Yasuo Saijo, Masanori Tsuchida, Mitsuo Nakayama, Koichi Hagiwara
Molecular targeting therapy for non-small cell lung cancer (NSCLC) has clarified the importance of mutation testing when selecting treatment regimens. As a result, multiple-gene mutation tests are urgently needed. We developed a next-generation sequencer (NGS)-based, multi-gene test named the MINtS for investigating driver mutations in both cytological specimens and snap-frozen tissue samples. The MINtS was used to investigate the EGFR, KRAS, BRAF genes from DNA, and the ERBB2, and the ALK, ROS1, and RET fusion genes from RNA...
2017: PloS One
https://www.readbyqxmd.com/read/28447410/2016-who-classification-update-what-s-new-in-lymphoid-neoplasms
#8
REVIEW
E D Hsi
In the 8 years since the publication of the 4th edition of the WHO Classification of Hematopoietic and Lymphoid Tumours in 2008, there has been rapid accumulation of knowledge in the molecular genetics, biology, clinical behavior of many hematologic malignancies. Concepts and models have advanced to the point at which updates were deemed necessary prior to the formal WHO process of publication of a 5th edition as part of the WHO "blue book" series. This overview will focus on lymphoid tumors and highlight important changes and updates to these neoplasms...
May 2017: International Journal of Laboratory Hematology
https://www.readbyqxmd.com/read/28447100/f7-gene-variants-modulate-protein-levels-in-a-large-cohort-of-patients-with-factor-vii-deficiency-results-from-a-genotype-phenotype-study
#9
Gabriele Quintavalle, Federica Riccardi, Gianna Franca Rivolta, Davide Martorana, Caterina Di Perna, Antonio Percesepe, Annarita Tagliaferri
Congenital factor VII (FVII) deficiency is a rare bleeding disorder caused by mutations in F7 gene with autosomal recessive inheritance. A clinical heterogeneity with poor correlation with FVII:C levels has been described. It was the objective of this study to identify genetic defects and to evaluate their relationships with phenotype in a large cohort of patients with FVII:C<50 %. One hundred twenty-three probands were genotyped for F7 mutations and three polymorphic variants and classified according to recently published clinical scores...
April 27, 2017: Thrombosis and Haemostasis
https://www.readbyqxmd.com/read/28446798/novel-missense-mutation-in-dll4-in-a-japanese-sporadic-case-of-adams-oliver-syndrome
#10
Miwako Nagasaka, Mariko Taniguchi-Ikeda, Hidehito Inagaki, Yuya Ouchi, Daisuke Kurokawa, Keiji Yamana, Risa Harada, Kandai Nozu, Yoshitada Sakai, Sushil K Mishra, Yoshiki Yamaguchi, Ichiro Morikoka, Tatsushi Toda, Hiroki Kurahashi, Kazumoto Iijima
Adams-Oliver syndrome (AOS, OMIM; 100300) is a rare genetic disease characterized by aplasia cutis congenita, terminal transverse limb defects and cutis marmorata with vascular anomalies such as congenital heart defects. The etiology of this syndrome has remained largely unknown but defective Notch signaling during vascular formation has been suggested. Here we describe a sporadic Japanese newborn case with clinically diagnosed AOS. Trio whole-exome sequencing identified a de novo, novel, heterozygous missense mutation in the Delta-like 4 ligand gene (DLL4 c...
April 27, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28445233/preclinical-models-for-translational-sarcoma-research
#11
Rainer Hamacher, Sebastian Bauer
PURPOSE OF REVIEW: Sarcoma is a basket term for mesenchymal tumors for which more than 75 genetically and histologically distinct subtypes are recognized. Therapeutic progress has largely been achieved with classical chemotherapeutic drugs that were tested in empirical clinical trials. However, outcome in metastatic patients remains poor and with few exceptions numerous trials have failed or only provided limited improvement in recent years. RECENT FINDINGS: Given the genomic heterogeneity, preclinical model systems will be indispensable to identify new molecular targets and to prioritize drugs and drug combinations...
April 25, 2017: Current Opinion in Oncology
https://www.readbyqxmd.com/read/28444624/targeting-ntrk-fusion-in-non-small-cell-lung-cancer-rationale-and-clinical-evidence
#12
REVIEW
Biagio Ricciuti, Marta Brambilla, Giulio Metro, Sara Baglivo, Roberta Matocci, Matteo Pirro, Rita Chiari
In the era of personalized medicine, the identification of targetable genetic alterations represented a major step forward in anticancer therapy. NTRK rearrangements represent the molecular driver of a subset of solid tumors, including 3% of non-small-cell lung cancers (NSCLCs). Preliminary data indicate that molecularly selected NSCLC patients harboring NTRK fusions derive an unprecedented clinical benefit from Trk-directed targeted therapies. The aim of this review is to describe the molecular biology of NTRK signaling pathway and to summarize the preclinical data on novel Trk inhibitors, touching upon the clinical development of these inhibitors for the treatment of advanced NSCLC, which have already shown encouraging anticancer activity and acceptable safety profile in early phase I clinical trials...
June 2017: Medical Oncology
https://www.readbyqxmd.com/read/28442916/expression-and-activity-of-the-urokinase-plasminogen-activator-system-in-canine-primary-brain-tumors
#13
John H Rossmeisl, Kelli Hall-Manning, John L Robertson, Jamie N King, Rafael V Davalos, Waldemar Debinski, Subbiah Elankumaran
BACKGROUND: The expression of the urokinase plasminogen activator receptor (uPAR), a glycosylphosphatidylinositol-anchored protein family member, and the activity of its ligand, urokinase-type plasminogen activator (uPA), have been associated with the invasive and metastatic potentials of a variety of human brain tumors through their regulation of extracellular matrix degradation. Domesticated dogs develop naturally occurring brain tumors that share many clinical, phenotypic, molecular, and genetic features with their human counterparts, which has prompted the use of the dogs with spontaneous brain tumors as models to expedite the translation of novel brain tumor therapeutics to humans...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28442527/a-novel-fibrillin-1-gene-mutation-leading-to-marfan-syndrome-in-a-korean-girl
#14
Hyo-Kyoung Nam, Myung-Hyun Nam, Kee-Soo Ha, Young-Jun Rhie, Kee-Hyoung Lee
Marfan syndrome is an autosomal dominant genetic disorder caused by a connective tissue defect. A nine-year-old girl was referred to our pediatric endocrinology clinic for tall stature. Physical examination revealed a lens dislocation with strabismus, high palate, positive wrist and thumb signs, joint hypermobility, and pes planus. Transthoracic echocardiography revealed dilatation of the aortic root. She was diagnosed with Marfan syndrome based on the revised Ghent diagnostic criteria. Molecular investigation identified a heterozygous c...
March 2017: Annals of Clinical and Laboratory Science
https://www.readbyqxmd.com/read/28442525/korean-monozygotic-twins-with-lethal-acantholytic-epidermolysis-bullosa-caused-by-two-novel-dsp-mutations
#15
Se Jin Kim, Jung Min Ko, Seung Han Shin, Ee-Kyung Kim, Han-Suk Kim, Kyung-A Lee
Desmoplakin is an essential cytoplasmic plaque protein in desmosomes, and it is the major linker between intercellular junctions in the skin and heart. The role of desmoplakin is anchoring transmembrane cadherins to cytoplasmic intermediate filaments. The desmoplakin gene (DSP) is located on chromosome 6, and six common allelic disorders are associated with this gene, including autosomal-dominant or -recessive disorders that affect the skin, heart, hair, and nails. In particular, lethal acantholytic epidermolysis bullosa (LAEB) is an autosomal recessively inherited and extremely rare genetic skin disorder, and only three molecularly confirmed families with LAEB have been reported previously...
March 2017: Annals of Clinical and Laboratory Science
https://www.readbyqxmd.com/read/28441150/long-non-coding-rnas-in-leukemia-biology-and-clinical-impact
#16
Tim Lammens, Kaat Durinck, Annelynn Wallaert, Frank Speleman, Pieter Van Vlierberghe
PURPOSE OF REVIEW: Over the last years, long non-coding RNAs (lncRNAs) have emerged as putative regulators of malignant hematopoietic development. Here, we review recent literature on the involvement of lncRNAs in leukemia, including their role in driving or sustaining disease and their potential impact on diagnosis, classification, and prognosis. RECENT FINDINGS: Leukemogenesis is a complex process resulting from the accumulation of multiple genetic alterations...
April 22, 2017: Current Opinion in Hematology
https://www.readbyqxmd.com/read/28440899/lissencephaly-expanded-imaging-and-clinical-classification
#17
Nataliya Di Donato, Sara Chiari, Ghayda M Mirzaa, Kimberly Aldinger, Elena Parrini, Carissa Olds, A James Barkovich, Renzo Guerrini, William B Dobyns
Lissencephaly ("smooth brain," LIS) is a malformation of cortical development associated with deficient neuronal migration and abnormal formation of cerebral convolutions or gyri. The LIS spectrum includes agyria, pachygyria, and subcortical band heterotopia. Our first classification of LIS and subcortical band heterotopia (SBH) was developed to distinguish between the first two genetic causes of LIS-LIS1 (PAFAH1B1) and DCX. However, progress in molecular genetics has led to identification of 19 LIS-associated genes, leaving the existing classification system insufficient to distinguish the increasingly diverse patterns of LIS...
April 25, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28440827/molecular-dynamics-investigations-of-membrane-bound-cyp2c19-polymorphisms-reveal-distinct-mechanisms-for-peripheral-variants-by-long-range-effects-on-the-enzymatic-activity
#18
Ying-Lu Cui, Rong-Ling Wu
Increasing sophistication in methods used to account for human polymorphisms in susceptibility to drug metabolism has been one of the success stories in the prevention of adverse drug reactions. Genetic polymorphisms in drug-metabolizing enzymes can affect enzyme activity and cause differences in treatment response or drug toxicity. CYP2C19 is one of the most highly polymorphic CYP enzymes and acts on 10-15% of drugs in current clinical use. Despite the number of experimental analyses carried out for this system, the detailed structural basis for altered catalytic properties of polymorphic CYP2C19 variants remains unexplained at the atomic level...
April 25, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28440781/immunohistochemical-detection-of-the-braf-v600e-mutation-in-papillary-thyroid-carcinoma-evaluation-against-real-time-polymerase-chain-reaction
#19
Miguel Paja Fano, Aitziber Ugalde Olano, Elena Fuertes Thomas, Amelia Oleaga Alday
INTRODUCTION: The BRAF V600E mutation is the most common genetic change in papillary thyroid carcinoma and is associated with a poorer clinical course. Usual methods for its study (DNA sequencing or molecular test based on PCR) are expensive and time-consuming. Recently, immunohistochemistry (IHC) for BRAF mutation has been introduced. OBJECTIVE: To compare the results of IHC and real time PCR (RT-PCR) in the detection of BRAF V600E mutation in papillary thyroid carcinoma...
February 2017: Endocrinol Diabetes Nutr
https://www.readbyqxmd.com/read/28439535/a-murine-preclinical-syngeneic-transplantation-model-for-breast-cancer-precision-medicine
#20
Lorenzo Federico, Zechen Chong, Dong Zhang, Daniel J McGrail, Wei Zhao, Kang Jin Jeong, Christopher P Vellano, Zhenlin Ju, Mihai Gagea, Shuying Liu, Shreya Mitra, Jennifer B Dennison, Philip L Lorenzi, Robert Cardnell, Lixia Diao, Jing Wang, Yiling Lu, Lauren A Byers, Charles M Perou, Shiaw-Yih Lin, Gordon B Mills
We previously demonstrated that altered activity of lysophosphatidic acid in murine mammary glands promotes tumorigenesis. We have now established and characterized a heterogeneous collection of mouse-derived syngeneic transplants (MDSTs) as preclinical platforms for the assessment of personalized pharmacological therapies. Detailed molecular and phenotypic analyses revealed that MDSTs are the most heterogeneous group of genetically engineered mouse models (GEMMs) of breast cancer yet observed. Response of MDSTs to trametinib, a mitogen-activated protein kinase (MAPK) kinase inhibitor, correlated with RAS/MAPK signaling activity, as expected from studies in xenografts and clinical trials providing validation of the utility of the model...
April 2017: Science Advances
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