1. Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates.

    Science advances 2(8):e1600633 (2016) PMID 27532052

    Colugos are among the most poorly studied mammals despite their centrality to resolving supraordinal primate relationships. Two described species of these gliding mammals are the sole living members of the order Dermoptera, distributed throughout Southeast Asia. We generated a draft genome seque...
  2. Comprehensive genomic analysis reveals FLT3 activation and a therapeutic strategy for a patient with relapsed adult B-lymphoblastic leukemia.

    Experimental Hematology 44(7):603 (2016) PMID 27181063 PMCID PMC4914477

    The genomic events responsible for the pathogenesis of relapsed adult B-lymphoblastic leukemia (B-ALL) are not yet clear. We performed integrative analysis of whole-genome, whole-exome, custom capture, whole-transcriptome (RNA-seq), and locus-specific genomic assays across nine time points from ...
  3. Genetic alterations in uncommon low-grade neuroepithelial tumors: BRAF, FGFR1, and MYB mutations occur at high frequency and align with morphology.

    Acta Neuropathologica 131(6):833 (2016) PMID 26810070 PMCID PMC4866893

    Low-grade neuroepithelial tumors (LGNTs) are diverse CNS tumors presenting in children and young adults, often with a history of epilepsy. While the genetic profiles of common LGNTs, such as the pilocytic astrocytoma and 'adult-type' diffuse gliomas, are largely established, those of uncommon LG...
  4. The Contribution of GWAS Loci in Familial Dyslipidemias.

    PLoS Genetics 12(5):e1006078 (2016) PMID 27227539 PMCID PMC4882070

    Familial combined hyperlipidemia (FCH) is a complex and common familial dyslipidemia characterized by elevated total cholesterol and/or triglyceride levels with over five-fold risk of coronary heart disease. The genetic architecture and contribution of rare Mendelian and common variants to FCH s...
  5. Inactivation of RASA1 promotes melanoma tumorigenesis via R-Ras activation.

    Oncotarget 7(17):23885 (2016) PMID 26993606

    Inactivation of Ras GTPase activating proteins (RasGAPs) can activate Ras, increasing the risk for tumor development. Utilizing a melanoma whole genome sequencing (WGS) data from 13 patients, we identified two novel, clustered somatic missense mutations (Y472H and L481F) in RASA1 (RAS p21 protei...
  6. Long-read sequence assembly of the gorilla genome.

    Science 352(6281):aae0344 (2016) PMID 27034376 PMCID PMC4920363

    Accurate sequence and assembly of genomes is a critical first step for studies of genetic variation. We generated a high-quality assembly of the gorilla genome using single-molecule, real-time sequence technology and a string graph de novo assembly algorithm. The new assembly improves contiguity...
  7. Rapid expansion of preexisting nonleukemic hematopoietic clones frequently follows induction therapy for de novo AML.

    Blood 127(7):893 (2016) PMID 26631115 PMCID PMC4760092

    There is interest in using leukemia-gene panels and next-generation sequencing to assess acute myelogenous leukemia (AML) response to induction chemotherapy. Studies have shown that patients with AML in morphologic remission may continue to have clonal hematopoiesis with populations closely rela...
  8. DGIdb 2.0: mining clinically relevant drug-gene interactions.

    Nucleic Acids Research 44(D1):D1036 (2016) PMID 26531824 PMCID PMC4702839

    The Drug-Gene Interaction Database (DGIdb, www.dgidb.org) is a web resource that consolidates disparate data sources describing drug-gene interactions and gene druggability. It provides an intuitive graphical user interface and a documented application programming interface (API) for querying th...
  9. The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling.

    Genome Biology and Evolution 8(1):109 (2016) PMID 26615215 PMCID PMC4758236

    Physarum polycephalum is a well-studied microbial eukaryote with unique experimental attributes relative to other experimental model organisms. It has a sophisticated life cycle with several distinct stages including amoebal, flagellated, and plasmodial cells. It is unusual in switching between ...
  10. Dictyocaulus viviparus genome, variome and transcriptome elucidate lungworm biology and support future intervention.

    Scientific reports 6:20316 (2016) PMID 26856411 PMCID PMC4746573

    The bovine lungworm, Dictyocaulus viviparus (order Strongylida), is an important parasite of livestock that causes substantial economic and production losses worldwide. Here we report the draft genome, variome, and developmental transcriptome of D. viviparus. The genome (161 Mb) is smaller than ...
  11. INTEGRATE: gene fusion discovery using whole genome and transcriptome data.

    Genome Research 26(1):108 (2016) PMID 26556708 PMCID PMC4691743

    While next-generation sequencing (NGS) has become the primary technology for discovering gene fusions, we are still faced with the challenge of ensuring that causative mutations are not missed while minimizing false positives. Currently, there are many computational tools that predict structural...
  12. Opsin Repertoire and Expression Patterns in Horseshoe Crabs: Evidence from the Genome of Limulus polyphemus (Arthropoda: Chelicerata).

    Genome Biology and Evolution 8(5):1571 (2016) PMID 27189985 PMCID PMC4898813

    Horseshoe crabs are xiphosuran chelicerates, the sister group to arachnids. As such, they are important for understanding the most recent common ancestor of Euchelicerata and the evolution and diversification of Arthropoda. Limulus polyphemus is the most investigated of the four extant species o...
  13. Identification of a Novel Gene on 10q22.1 Causing Autosomal Dominant Retinitis Pigmentosa (adRP).

    Advances in Experimental Medicine and Biology 854:193 (2016) PMID 26427411 PMCID PMC4906966

    Whole-genome linkage mapping identified a region on chromosome 10q21.3-q22.1 with a maximum LOD score of 3.0 at 0 % recombination in a six-generation family with autosomal dominant retinitis pigmentosa (adRP). All known adRP genes and X-linked RP genes were excluded in the family by a combinatio...
  14. Aromatase inhibition remodels the clonal architecture of estrogen-receptor-positive breast cancers.

    Nature Communications 7:12498 (2016) PMID 27502118 PMCID PMC4980485

    Resistance to oestrogen-deprivation therapy is common in oestrogen-receptor-positive (ER+) breast cancer. To better understand the contributions of tumour heterogeneity and evolution to resistance, here we perform comprehensive genomic characterization of 22 primary tumours sampled before and af...
  15. A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination.

    G3: Genes, Genomes, Genetics 6(6):1607 (2016) PMID 27172201 PMCID PMC4889657

    High-resolution genetic and physical maps are invaluable tools for building accurate genome assemblies, and interpreting results of genome-wide association studies (GWAS). Previous genetic and physical maps anchored good quality draft assemblies of the domestic cat genome, enabling the discovery...
  16. Germline Mutations in Predisposition Genes in Pediatric Cancer.

    New England Journal of Medicine 373(24):2336 (2015) PMID 26580448 PMCID PMC4734119

    The prevalence and spectrum of predisposing mutations among children and adolescents with cancer are largely unknown. Knowledge of such mutations may improve the understanding of tumorigenesis, direct patient care, and enable genetic counseling of patients and families. In 1120 patients younger ...
  17. Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection.
    Rafael D Mesquita, Raquel J Vionette-Amaral, Carl Lowenberger, Rolando Rivera-Pomar, Fernando A Monteiro, Patrick Minx, John Spieth, A Bernardo Carvalho, Francisco Panzera, Daniel Lawson, André Q Torres, Jose M C Ribeiro, Marcos H F Sorgine, Robert M Waterhouse, Michael J Montague, Fernando Abad-Franch, Michele Alves-Bezerra, Laurence R Amaral, Helena M Araujo, Ricardo N Araujo, L Aravind, Georgia C Atella, Patricia Azambuja, Mateus Berni, Paula R Bittencourt-Cunha, Gloria R C Braz, Gustavo Calderón-Fernández, Claudia M A Carareto, Mikkel B Christensen, Igor R Costa, Samara G Costa, Marilvia Dansa, Carlos R O Daumas-Filho, Iron F De-Paula, Felipe A Dias, George Dimopoulos, Scott J Emrich, Natalia Esponda-Behrens, Patricia Fampa, Rita D Fernandez-Medina, Rodrigo N da Fonseca, Marcio Fontenele, Catrina Fronick, Lucinda A Fulton, Ana Caroline Gandara, Eloi S Garcia, Fernando A Genta, Gloria I Giraldo-Calderón, Bruno Gomes, Katia C Gondim, Adriana Granzotto, Alessandra Guarneri, Roderic Guigó, Myriam Harry, Daniel S T Hughes, Willy Jablonka, Emmanuelle, M Patricia Juárez, Leonardo B Koerich, Angela B Lange, José Manuel Latorre-Estivalis, Andrés Lavore, Gena Lawrence, Cristiano Lazoski, Claudio R Lazzari, Raphael Lopes, Marcelo G Lorenzo, Magda D Lugon, David Majerowicz, Paula L Marcet, Marco Mariotti, Hatisaburo Masuda, Karine Megy, Ana C Melo, Fanis Missirlis, Theo Mota, Fernando G Noriega, Marcela Nouzova, Rodrigo D Nunes, Raquel L Oliveira, Gilbert Oliveira-Silveira, Sheila Ons, Ian Orchard, Lucia Pagola, Gabriela O Paiva-Silva, Agustina Pascual, Marcio G Pavan, Nicolás Pedrini, Alexandre Peixoto, Marcos H Pereira, Andrew Pike, Carla Polycarpo, Francisco Prosdocimi, Rodrigo, Hugh M Robertson, Ana Paula Salerno, Didier Salmon, Didac Santesmasses, Renata Schama, Eloy Seabra-Junior, Livia Silva-Cardoso, Mario A C Silva-Neto, Matheus Souza-Gomes, Marcos Sterkel, Mabel L Taracena, Marta Tojo, Zhijian Jake Tu, Jose M C Tubio, Raul Ursic-Bedoya, Thiago M Venancio, Ana Beatriz Walter-Nuno, Derek Wilson, Wesley C Warren, Richard K Wilson, Erwin Huebner, Ellen M Dotson, and Pedro L Oliveira

    PNAS 112(48):14936 (2015) PMID 26627243 PMCID PMC4672799

    Rhodnius prolixus not only has served as a model organism for the study of insect physiology, but also is a major vector of Chagas disease, an illness that affects approximately seven million people worldwide. We sequenced the genome of R. prolixus, generated assembled sequences covering 95% of ...
  18. The genome of the vervet (Chlorocebus aethiops sabaeus).

    Genome Research 25(12):1921 (2015) PMID 26377836 PMCID PMC4665013

    We describe a genome reference of the African green monkey or vervet (Chlorocebus aethiops). This member of the Old World monkey (OWM) superfamily is uniquely valuable for genetic investigations of simian immunodeficiency virus (SIV), for which it is the most abundant natural host species, and o...
  19. Cracking the nodule worm code advances knowledge of parasite biology and biotechnology to tackle major diseases of livestock.

    Biotechnology Advances 33(6 Pt 1):980 (2015) PMID 26026709 PMCID PMC4746232

    Many infectious diseases caused by eukaryotic pathogens have a devastating, long-term impact on animal health and welfare. Hundreds of millions of animals are affected by parasitic nematodes of the order Strongylida. Unlocking the molecular biology of representatives of this order, and understan...
  20. Genetic variation and the de novo assembly of human genomes.

    Nature Reviews: Genetics 16(11):627 (2015) PMID 26442640 PMCID PMC4745987

    The discovery of genetic variation and the assembly of genome sequences are both inextricably linked to advances in DNA-sequencing technology. Short-read massively parallel sequencing has revolutionized our ability to discover genetic variation but is insufficient to generate high-quality genome...