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1. Full Text Comment on “DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification”
by Stewart, Chip and Leshchiner, Ignaty and Hess, Julian and Getz, Gad
Science, ISSN 0036-8075, 09/2018, Volume 361, Issue 6409, p. eaas9824
DNA damage | Deoxyribonucleic acid--DNA | DNA sequencing | Gene sequencing
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2. Full Text Resensitization to Crizotinib by the Lorlatinib ALK Resistance Mutation L1198F
by Shaw, Alice T and Friboulet, Luc and Leshchiner, Ignaty and Gainor, Justin F and Bergqvist, Simon and Brooun, Alexei and Burke, Benjamin J and Deng, Ya-Li and Liu, Wei and Dardaei, Leila and Frias, Rosa L and Schultz, Kate R and Logan, Jennifer and James, Leonard P and Smeal, Tod and Timofeevski, Sergei and Katayama, Ryohei and Iafrate, A. John and Le, Long and McTigue, Michele and Getz, Gad and Johnson, Ted W and Engelman, Jeffrey A and Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
The New England Journal of Medicine, ISSN 0028-4793, 01/2016, Volume 374, Issue 1, pp. 54 - 61
A resistance mutation (C1156Y) developed in a woman with anaplastic lymphoma kinase ( ALK )-rearranged lung cancer who had a response to crizotinib. She then... 
Liver Failure - etiology | Lung Neoplasms - genetics | Lung Neoplasms - drug therapy | Sulfones - therapeutic use | Pyrazoles - therapeutic use | Carcinoma, Non-Small-Cell Lung - genetics | Humans | Middle Aged | Drug Resistance, Neoplasm - genetics | Carcinoma, Non-Small-Cell Lung - secondary | Receptor Protein-Tyrosine Kinases - genetics | Protein Kinase Inhibitors - therapeutic use | Pyrimidines - therapeutic use | Receptor Protein-Tyrosine Kinases - antagonists & inhibitors | Female | Molecular Structure | Carcinoma, Non-Small-Cell Lung - drug therapy | Lactams, Macrocyclic - therapeutic use | Mutation | Liver Neoplasms - secondary | Binding Sites | Pyridines - therapeutic use | Crizotinib | Gene mutations | Analysis | Lung cancer | Dosage and administration | Research | Drug resistance | Drug therapy | Tyrosine | Inhibitor drugs | Liver diseases | Genes | Lymphoma | Cancer therapies | Metastases | Amino acid substitution | Liver cancer | Protein-tyrosine kinase | Cancer | Index Medicus | Abridged Index Medicus
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3. Full Text Comprehensive assessment of cancer missense mutation clustering in protein structures
by Atanas Kamburov and Michael S. Lawrence and Paz Polak and Ignaty Leshchiner and Kasper Lage and Todd R. Golub and Eric S. Lander and Gad Getz
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 10/2015, Volume 112, Issue 40, pp. E5486 - E5495
Large-scale tumor sequencing projects enabled the identification of many new cancer gene candidates through computational approaches. Here, we describe a... 
Cancer genetics | Mutation clustering | Interaction interfaces | Protein structures | Cancer | COMPLEX | RECOGNITION | KINETOCHORE | CRYSTAL-STRUCTURE | MULTIDISCIPLINARY SCIENCES | protein structures | SOMATIC MUTATIONS | LUNG-CANCER | cancer genetics | DNA | GROWTH | mutation clustering | SPOP | TUMOR-SUPPRESSOR | cancer | interaction interfaces | Neoplasms - metabolism | Protein Structure, Tertiary | Oncogene Proteins - genetics | Catalytic Domain | Genetic Predisposition to Disease - genetics | Oncogene Proteins - chemistry | Humans | Cell Cycle Proteins - metabolism | Oncogene Proteins - metabolism | Models, Molecular | Mutation, Missense | Cell Cycle Proteins - chemistry | Protein Interaction Mapping - methods | Algorithms | Neoplasms - genetics | Protein Interaction Maps - genetics | Databases, Protein | Cell Cycle Proteins - genetics | Protein Binding | Cluster Analysis | Proteins | Gene mutations | Genetic aspects | Metastasis | Observations | Tumor proteins | Structure | Health aspects | Mutation | Molecular structure | Tumors | Index Medicus | Biological Sciences | PNAS Plus
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4. Full Text Paired exome analysis of Barrett's esophagus and adenocarcinoma
by Stachler, Matthew D and Taylor-Weiner, Amaro and Peng, Shouyong and McKenna, Aaron and Agoston, Agoston T and Odze, Robert D and Davison, Jon M and Nason, Katie S and Loda, Massimo and Leshchiner, Ignaty and Stewart, Chip and Stojanov, Petar and Seepo, Sara and Lawrence, Michael S and Ferrer-Torres, Daysha and Lin, Jules and Chang, Andrew C and Gabriel, Stacey B and Lander, Eric S and Beer, David G and Getz, Gad and Carter, Scott L and Bass, Adam J
Nature Genetics, ISSN 1061-4036, 08/2015, Volume 47, Issue 9, pp. 1047 - 1055
Barrett's esophagus is thought to progress to esophageal adenocarcinoma (EAC) through a stepwise progression with loss of CDKN2A followed by TP53 inactivation... 
GENOMIC INSTABILITY | GASTROESOPHAGEAL-REFLUX | HIGH-GRADE DYSPLASIA | NEOPLASTIC PROGRESSION | CLONAL EXPANSION | PROSTATE-CANCER | COPY NUMBER | PANCREATIC-CANCER | GENETICS & HEREDITY | CIRCULAR BINARY SEGMENTATION | SOMATIC MUTATIONS | Genetic Predisposition to Disease | Genome-Wide Association Study | Gene Frequency | Humans | Cyclin-Dependent Kinase Inhibitor p16 - genetics | Tumor Suppressor Protein p53 - genetics | Exome | Phosphatidylinositol 3-Kinases - genetics | Point Mutation | Class I Phosphatidylinositol 3-Kinases | Gene Amplification | Esophageal Neoplasms - genetics | DNA Mutational Analysis | Adenocarcinoma - genetics | Barrett Esophagus - genetics | Usage | Genetic aspects | Diagnosis | Research | Barrett's esophagus | Exome sequencing | Datasets | Cloning | Genomes | Mutation | Endoscopy | Patients | Impaired risk | Cancer | Index Medicus
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5. Full Text Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes
by Chapuy, Bjoern and Stewart, Chip and Dunford, Andrew J and Kim, Jaegil and Kamburov, Atanas and Redd, Robert A and Lawrence, Mike S and Roemer, Margaretha G. M and Li, Amy J and Ziepert, Marita and Staiger, Annette M and Wala, Jeremiah A and Ducar, Matthew D and Leshchiner, Ignaty and Rheinbay, Ester and Taylor-Weiner, Amaro and Coughlin, Caroline A and Hess, Julian M and Pedamallu, Chandra S and Livitz, Dimitri and Rosebrock, Daniel and Rosenberg, Mara and Tracy, Adam A and Horn, Heike and Van Hummelen, Paul and Feldman, Andrew L and Link, Brian K and Novak, Anne J and Cerhan, James R and Habermann, Thomas M and Siebert, Reiner and Rosenwald, Andreas and Thorner, Aaron R and Meyerson, Matthew L and Golub, Todd R and Beroukhim, Rameen and Wulf, Gerald G and Ott, German and Rodig, Scott J and Monti, Stefano and Neuberg, Donna S and Loeffler, Markus and Pfreundschuh, Michael and Trümper, Lorenz and Getz, Gad and Shipp, Margaret A
Nature Medicine, ISSN 1078-8956, 05/2018, Volume 24, Issue 5, pp. 679 - 690
Diffuse large B cell lymphoma (DLBCL), the most common lymphoid malignancy in adults, is a clinically and genetically heterogeneous disease that is further... 
MEDICINE, RESEARCH & EXPERIMENTAL | BIOCHEMISTRY & MOLECULAR BIOLOGY | FOLLICULAR LYMPHOMA | SOMATIC MUTATIONS | DISCOVERY | CELL BIOLOGY | INTEGRATIVE ANALYSIS REVEALS | CODING GENOME | GENES | NON-HODGKIN-LYMPHOMA | MARGINAL ZONE LYMPHOMA | DNA-SEQUENCING DATA | HUMAN CANCER | Lymphoma, Large B-Cell, Diffuse - pathology | Genes, Neoplasm | Humans | Mutation Rate | Treatment Outcome | DNA Copy Number Variations - genetics | Gene Rearrangement - genetics | Mutation - genetics | Lymphoma, Large B-Cell, Diffuse - genetics | Genetic Heterogeneity | Oncology, Experimental | Development and progression | Genetic aspects | Non-Hodgkin's lymphomas | B cells | Research | Identification and classification | Health aspects | Cancer | Stability | Deactivation | Transcription | Risk groups | Pathogenesis | Copy number | p53 Protein | Malignancy | Inactivation | Clustering | Lymphoma | Molecular chains | Genomic instability | Alterations | Lymphocytes B | Genetic analysis | New combinations | Lymphomas | Adults | Mutation | Signatures | B-cell lymphoma | Index Medicus
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6. Full Text A mutational signature reveals alterations underlying deficient homologous recombination repair in breast cancer
by Polak, Paz and Kim, Jaegil and Braunstein, Lior Z and Karlic, Rosa and Haradhavala, Nicholas J and Tiao, Grace and Rosebrock, Daniel and Livitz, Dimitri and Kübler, Kirsten and Mouw, Kent W and Kamburov, Atanas and Maruvka, Yosef E and Leshchiner, Ignaty and Lander, Eric S and Golub, Todd R and Zick, Aviad and Orthwein, Alexandre and Lawrence, Michael S and Batra, Rajbir N and Caldas, Carlos and Haber, Daniel A and Laird, Peter W and Shen, Hui and Ellisen, Leif W and D'Andrea, Alan D and Chanock, Stephen J and Foulkes, William D and Getz, Gad
Nature Genetics, ISSN 1061-4036, 10/2017, Volume 49, Issue 10, pp. 1476 - 1486
Biallelic inactivation of BRCA1 or BRCA2 is associated with a pattern of genome-wide mutations known as signature 3. By analyzing similar to 1,000 breast... 
COMPREHENSIVE MOLECULAR PORTRAITS | SEQUENCE VARIATION | VARIANTS | LANDSCAPE | SUSCEPTIBILITY | GENETICS & HEREDITY | OVARIAN-CANCER | PARP INHIBITORS | FAMILY-HISTORY | TUMORS | GERMLINE BRCA1 MUTATIONS | Genetic Predisposition to Disease | Gene Regulatory Networks - genetics | Recombinational DNA Repair - genetics | Genes, Neoplasm | Humans | Gene Silencing | Transcriptome - genetics | Allelic Imbalance | DNA Methylation | Breast Neoplasms - genetics | Genes, BRCA2 | Germ-Line Mutation | Female | Genes, BRCA1 | Mutation | Neoplasm Proteins - genetics | Gene Expression Regulation, Neoplastic - genetics | Care and treatment | Gene mutations | Development and progression | Breast cancer | Genetic aspects | Genetic recombination | Health aspects | BRCA2 protein | Deactivation | BRCA1 protein | Genomics | Homologous recombination | Homology | Genomes | Gene expression | Inactivation | Ovarian cancer | Homologous recombination repair | Cell cycle | DNA methylation | Epigenetics | Breast | Methylation | Signatures | Deoxyribonucleic acid--DNA | Cancer | Tumors | Index Medicus
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7. Full Text Summarizing polygenic risks for complex diseases in a clinical whole-genome report
by Kong, Sek Won and Lee, In-Hee and Leshchiner, Ignaty and Krier, Joel and Kraft, Peter and Rehm, Heidi L and Green, Robert C and Kohane, Isaac S and Macrae, Calum A and Bates, David W and Carere, Alexis D and Cirino, Allison and Connor, Lauren and Christensen, Kurt D and Duggan, Jake and Ho, Carolyn Y and Krier, Joel B and Lane, William J and Lautenbach, Denise M and Lehmann, Lisa and Liu, Christina and Miller, Rachel and Morton, Cynthia C and Seidman, Christine E and Sunyaev, Shamil and Vassy, Jason L and Aronson, Sandy and Ceyhan-Birsoy, Ozge and Gowrisankar, Siva and Lebo, Matthew S and Leschiner, Ignat and Machini, Kalotina and McLaughlin, Heather M and Metterville, Danielle R and Blumenthal-Barby, Jennifer and Zausmer Feuerman, Lindsay and McGuire, Amy L and Panchang, Sarita and Robinson, Jill Oliver and Slashinski, Melody J and Alexander, Stewart C and Davis, Kelly and Ubel, Peter A and Roberts, J. Scott and Garber, Judy E and Hambuch, Tina and Murray, Michael F and MedSeq Project and the MedSeq Project
Genetics in Medicine, ISSN 1098-3600, 07/2015, Volume 17, Issue 7, pp. 536 - 544
Purpose: Disease-causing mutations and pharmacogenomic variants are of primary interest for clinical whole-genome sequencing. However, estimating genetic... 
risk alleles | polygenic score | clinical whole-genome sequencing | common complex disorders | CATALOG | GENETICS & HEREDITY | WIDE ASSOCIATION | CANCER | BREAST | PREDICTION | Cardiomyopathies - genetics | Multifactorial Inheritance - genetics | Genetic Predisposition to Disease | Genome-Wide Association Study | Reproducibility of Results | Genetic Association Studies | Humans | Alleles | Genome, Human | Genetic Testing - methods | Case-Control Studies | Index Medicus
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8. Full Text Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors
by Adalsteinsson, Viktor A and Ha, Gavin and Freeman, Samuel S and Choudhury, Atish D and Stover, Daniel G and Parsons, Heather A and Gydush, Gregory and Reed, Sarah C and Rotem, Denisse and Rhoades, Justin and Loginov, Denis and Livitz, Dimitri and Rosebrock, Daniel and Leshchiner, Ignaty and Kim, Jaegil and Stewart, Chip and Rosenberg, Mara and Francis, Joshua M and Zhang, Cheng-Zhong and Cohen, Ofir and Oh, Coyin and Ding, Huiming and Polak, Paz and Lloyd, Max and Mahmud, Sairah and Helvie, Karla and Merrill, Margaret S and Santiago, Rebecca A and O'Connor, Edward P and Jeong, Seong H and Leeson, Rachel and Barry, Rachel M and Kramkowski, Joseph F and Zhang, Zhenwei and Polacek, Laura and Lohr, Jens G and Schleicher, Molly and Lipscomb, Emily and Saltzman, Andrea and Oliver, Nelly M and Marini, Lori and Waks, Adrienne G and Harshman, Lauren C and Tolaney, Sara M and Van Allen, Eliezer M and Winer, Eric P and Lin, Nancy U and Nakabayashi, Mari and Taplin, Mary-Ellen and Johannessen, Cory M and Garraway, Levi A and Golub, Todd R and Boehm, Jesse S and Wagle, Nikhil and Getz, Gad and Love, J. Christopher and Meyerson, Matthew
Nature Communications, ISSN 2041-1723, 12/2017, Volume 8, Issue 1, pp. 1324 - 13
Whole-exome sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and... 
COMPREHENSIVE MOLECULAR PORTRAITS | BREAST-CANCER | LUNG-CANCER | EVOLUTION | SIGNATURES | MULTIDISCIPLINARY SCIENCES | PROSTATE-CANCER | PLASMA DNA | MUTATIONAL LANDSCAPE | CHRONIC LYMPHOCYTIC-LEUKEMIA | CIRCULAR BINARY SEGMENTATION | Profiling | Identification methods | Copy number | Genomes | Metastasis | Patients | Blood | Gene sequencing | Metastases | Mutation | Prostate | Deoxyribonucleic acid--DNA | Tumors | DNA sequencing | Index Medicus
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9. Full Text Loss of function mutation in LOX causes thoracic aortic aneurysm and dissection in humans
by Vivian S. Lee and Carmen M. Halabi and Erin P. Hoffman and Nikkola Carmichael and Ignaty Leshchiner and Christine G. Lian and Andrew J. Bierhals and Dana Vuzman and Brigham Genomic Medicine and Robert P. Mecham and Natasha Y. Frank and Nathan O. Stitziel and Brigham Genomic Med and Brigham Genomic Medicine
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 8/2016, Volume 113, Issue 31, pp. 8759 - 8764
Thoracic aortic aneurysms and dissections (TAAD) represent a substantial cause of morbidity and mortality worldwide. Many individuals presenting with an... 
CRISPR/Cas9 | whole-genome sequencing | MULTIDISCIPLINARY SCIENCES | MOUSE | CROSS-LINKING | lysyl oxidase | LYSYL-OXIDASE | BETA | HAPLOINSUFFICIENCY | ELASTOGENESIS | genetics | MARFAN-SYNDROME | ELASTIN | MICE | aortic dissection | EXPRESSION | Aneurysm, Dissecting - genetics | Aortic Aneurysm, Thoracic - genetics | Genetic Predisposition to Disease - genetics | Loss of Function Mutation | Aortic Aneurysm, Thoracic - enzymology | Humans | Mice, Inbred C57BL | Middle Aged | Family Health | Male | DNA Mutational Analysis - methods | Mice, Knockout | Aneurysm, Dissecting - enzymology | Animals | Pedigree | Base Sequence | Protein-Lysine 6-Oxidase - metabolism | Adult | Female | Aged | Protein-Lysine 6-Oxidase - genetics | Mortality | Genes | Collagen | Rodents | Aneurysms | Mutation | Hemorrhage | Index Medicus | Biological Sciences | CRISPR | Cas9
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10. Full Text Comment on "DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification"
by Stewart, Chip and Leshchiner, Ignaty and Hess, Julian and Getz, Gad
Science, ISSN 0036-8075, 09/2018, Volume 361, Issue 6409, p. 1324
Chen et al. (Reports, 17 February 2017, p. 752) highlight an important problem of sequencing artifacts caused by DNA damage at the time of sample processing.... 
INTEGRATED GENOMIC CHARACTERIZATION | LANDSCAPE | CARCINOMA | MULTIDISCIPLINARY SCIENCES | Artifacts | High-Throughput Nucleotide Sequencing | DNA Damage | Neoplasms - genetics | Sequence Analysis, DNA | Humans | DNA damage | Genomics | DNA | Causes of | Nucleotide sequencing | Analysis | DNA sequencing | Index Medicus
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11. Full Text The evolutionary landscape of chronic lymphocytic leukemia treated with ibrutinib targeted therapy
by Landau, Dan A and Sun, Clare and Rosebrock, Daniel and Herman, Sarah E. M and Fein, Joshua and Sivina, Mariela and Underbayev, Chingiz and Liu, Delong and Hoellenriegel, Julia and Ravichandran, Sarangan and Farooqui, Mohammed Z. H and Zhang, Wandi and Cibulskis, Carrie and Zviran, Asaf and Neuberg, Donna S and Livitz, Dimitri and Bozic, Ivana and Leshchiner, Ignaty and Getz, Gad and Burger, Jan A and Wiestner, Adrian and Wu, Catherine J
Nature Communications, ISSN 2041-1723, 12/2017, Volume 8, Issue 1, pp. 2185 - 12
Treatment of chronic lymphocytic leukemia (CLL) has shifted from chemo-immunotherapy to targeted agents. To define the evolutionary dynamics induced by... 
B-CELL LYMPHOMA | TUMOR-MICROENVIRONMENT | MULTIDISCIPLINARY SCIENCES | INITIAL THERAPY | RESISTANCE | CLONAL EVOLUTION | MUTATIONS | SEQUENCING DATA | SINGLE-ARM | GENOME | PROGRESSION | Pyrazoles - therapeutic use | Prognosis | Humans | Middle Aged | Male | Leukemia, Lymphocytic, Chronic, B-Cell - genetics | Clonal Evolution - genetics | Antineoplastic Combined Chemotherapy Protocols - pharmacology | Rituximab - therapeutic use | Phospholipase C gamma - genetics | Aged, 80 and over | Adult | Female | Gene Expression Regulation, Neoplastic - drug effects | Molecular Targeted Therapy - methods | Pyrazoles - pharmacology | Signal Transduction | Clonal Evolution - drug effects | Down-Regulation | Treatment Outcome | Pyrimidines - pharmacology | Disease Progression | Leukemia, Lymphocytic, Chronic, B-Cell - pathology | Whole Exome Sequencing | Rituximab - pharmacology | Drug Resistance, Neoplasm - genetics | Antineoplastic Combined Chemotherapy Protocols - therapeutic use | Pyrimidines - therapeutic use | Agammaglobulinaemia Tyrosine Kinase | Aged | Leukemia, Lymphocytic, Chronic, B-Cell - mortality | Leukemia, Lymphocytic, Chronic, B-Cell - drug therapy | Mutation | Longitudinal Studies | Drug Resistance, Neoplasm - drug effects | Protein-Tyrosine Kinases - antagonists & inhibitors | Lymphocyte receptors | Therapy | Energy metabolism | Chronic lymphatic leukemia | Transcription | Leukemia | Lymphatic leukemia | Metabolism | Drug resistance | Gene expression | Bruton's tyrosine kinase | Signaling | Lymphocytes B | Immunotherapy | Cell cycle | Evolution | Cancer | Index Medicus
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12. Full Text Mutations in RABL3 alter KRAS prenylation and are associated with hereditary pancreatic cancer
by Nissim, Sahar and Leshchiner, Ignaty and Mancias, Joseph D and Greenblatt, Matthew B and Maertens, Ophelia and Cassa, Christopher A and Rosenfeld, Jill A
Nature Genetics, ISSN 1061-4036, 09/2019, Volume 51, Issue 9, pp. 1308 - 1314
Usage | Care and treatment | Zebra fish | Pancreatic cancer | Genetic aspects | Nucleotide sequencing | Research | Mass spectrometry | DNA sequencing | Index Medicus
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13. Full Text Liquid versus tissue biopsy for detecting acquired resistance and tumor heterogeneity in gastrointestinal cancers
by Parikh, Aparna R and Leshchiner, Ignaty and Elagina, Liudmila and Goyal, Lipika and Levovitz, Chaya and Siravegna, Giulia and Livitz, Dimitri
Nature Medicine, ISSN 1078-8956, 09/2019, Volume 25, Issue 9, pp. 1415 - 1421
During cancer therapy, tumor heterogeneity can drive the evolution of multiple tumor subclones harboring unique resistance mechanisms in an individual... 
Therapy | Sequences | Autopsies | Data acquisition | Case reports | Heterogeneity | Alterations | Biopsy | Autopsy | Lesions | Target acquisition | Deoxyribonucleic acid--DNA | Tumors | Index Medicus
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14. Full Text Combinatorial approach to determine functional group effects on lipidoid-mediated siRNA delivery
by Mahon, Kerry P and Love, Kevin T and Whitehead, Kathryn A and Qin, June and Akinc, Akin and Leshchiner, Elizaveta and Leshchiner, Ignaty and Langer, Robert and Anderson, Daniel G
Bioconjugate Chemistry, ISSN 1043-1802, 08/2010, Volume 21, Issue 8, pp. 1448 - 1454
The application of RNA interference (RNAi), either in the clinic or in the laboratory, requires safe and effective delivery methods. Here, we develop a... 
RNA INTERFERENCE | IN-VIVO DELIVERY | BIOCHEMISTRY & MOLECULAR BIOLOGY | BIOCHEMICAL RESEARCH METHODS | CHEMISTRY, ORGANIC | CONJUGATE | SYSTEMS | DENDRIMERS | MAMMALIAN-CELLS | VECTORS | CHEMISTRY, MULTIDISCIPLINARY | NUCLEIC-ACIDS | Cell Survival - drug effects | Gene Transfer Techniques | Acrylates - chemistry | Genetic Vectors - chemistry | Humans | Mice, Inbred C57BL | RNA, Small Interfering - pharmacology | Acrylamides - chemistry | Dose-Response Relationship, Drug | RNA, Small Interfering - chemistry | Lipids - chemistry | Animals | Combinatorial Chemistry Techniques | Lipids - chemical synthesis | Mice | Molecular Structure | Factor VII - analysis | HeLa Cells | Lipids | Biochemistry | Ribonucleic acid--RNA | Biological assays | Cells | Index Medicus
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