Volume 23, Issue 9 | September 2013

Research
- - DNA methylation contributes to natural human variation
    Holger Heyn
    Sebastian Moran
    Irene Hernando-Herraez
    Sergi Sayols
    Antonio Gomez
    Juan Sandoval Dave Monk
    ...[+2 authors]...,
    Kenichiro Hata
    Tomas Marques-Bonet
    Liewei Wang
    Manel Esteller
    First Published August 1, 2013
  - Evolution and diversity of copy number variation in the great ape lineage
    Peter H. Sudmant
    John Huddleston
    Claudia R. Catacchio
    Maika Malig
    LaDeana W. Hillier
    Carl Baker Kiana Mohajeri Ivanela Kondova Ronald E. Bontrop Stephan Persengiev Francesca Antonacci
    ...[+6 authors]...,
    Mario Ventura
    Javier Prado-Martinez
    Tomas Marques-Bonet
    Evan E. Eichler
    First Published July 3, 2013
  - Deletions of recessive disease genes: CNV contribution to carrier states and disease-causing alleles
    Philip M. Boone
    Ian M. Campbell
    Brett C. Baggett
    Zachry T. Soens
    Mitchell M. Rao
    Patricia M. Hixson Ankita Patel Weimin Bi Sau Wai Cheung Seema R. Lalani
    ...[+5 authors]...,
    Arthur L. Beaudet
    Pawel Stankiewicz
    Chad A. Shaw
    James R. Lupski
    First Published May 16, 2013
  - NAHR-mediated copy-number variants in a clinical population: Mechanistic insights into both genomic disorders and Mendelizing traits
    Piotr Dittwald
    Tomasz Gambin
    Przemyslaw Szafranski
    Jian Li
    Stephen Amato
    Michael Y. Divon Lisa Ximena Rodríguez Rojas Lindsay E. Elton Daryl A. Scott Christian P. Schaaf Wilfredo Torres-Martinez Abby K. Stevens Jill A. Rosenfeld Satish Agadi David Francis Sung-Hae L. Kang Amy Breman Seema R. Lalani Carlos A. Bacino Weimin Bi Aleksandar Milosavljevic Arthur L. Beaudet Ankita Patel Chad A. Shaw
    ...[+19 authors]...,
    James R. Lupski
    Anna Gambin
    Sau Wai Cheung
    Pawel Stankiewicz
    First Published May 8, 2013
  - The complex SNP and CNV genetic architecture of the increased risk of congenital heart defects in Down syndrome
    M. Reza Sailani
    Periklis Makrythanasis
    Armand Valsesia
    Federico A. Santoni
    Samuel Deutsch
    Konstantin Popadin Christelle Borel Eugenia Migliavacca Andrew J. Sharp Genevieve Duriaux Sail Emilie Falconnet Kelly Rabionet Clara Serra-Juhé Stefano Vicari Daniela Laux Yann Grattau Guy Dembour Andre Megarbane Renaud Touraine Samantha Stora Sofia Kitsiou Helena Fryssira Chariklia Chatzisevastou-Loukidou Emmanouel Kanavakis Giuseppe Merla Damien Bonnet
    ...[+21 authors]...,
    Luis A. Pérez-Jurado
    Xavier Estivill
    Jean M. Delabar
    Stylianos E. Antonarakis
    First Published June 19, 2013
  - Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma
    Kan Zhengyan
    Zheng Hancheng
    Liu Xiao
    Li Shuyu
    Barber Thomas D.
    Gong Zhuolin Gao Huan Hao Ke Willard Melinda D. Xu Jiangchun Hauptschein Robert Rejto Paul A. Fernandez Julio Wang Guan Zhang Qinghui Wang Bo Chen Ronghua Wang Jian Lee Nikki P. Zhou Wei Lin Zhao Peng Zhiyu Yi Kang Chen Shengpei Li Lin Fan Xiaomei Yang Jie Ye Rui Ju Jia Wang Kai Estrella Heather Deng Shibing Wei Ping Qiu Ming Wulur Isabella H. Liu Jiangang Ehsani Mariam E. Zhang Chunsheng Loboda Andrey Sung Wing Kin Aggarwal Amit Poon Ronnie T. Fan Sheung Tat Wang Jun Hardwick James Reinhard Christoph
    ...[+41 authors]...,
    Dai Hongyue
    Li Yingrui
    Luk John M.
    Mao Mao
    First Published June 20, 2013
  - Next-generation sequencing of paired tyrosine kinase inhibitor-sensitive and -resistant EGFR mutant lung cancer cell lines identifies spectrum of DNA changes associated with drug resistance
    Peilin Jia
    Hailing Jin
    Catherine B. Meador
    Junfeng Xia
    Kadoaki Ohashi
    Lin Liu Valentina Pirazzoli Kimberly B. Dahlman
    ...[+3 authors]...,
    Katerina Politi
    Franziska Michor
    Zhongming Zhao
    William Pao
    First Published June 3, 2013
  - CCAT2, a novel noncoding RNA mapping to 8q24, underlies metastatic progression and chromosomal instability in colon cancer
    Hui Ling
    Riccardo Spizzo
    Yaser Atlasi
    Milena Nicoloso
    Masayoshi Shimizu
    Roxana S. Redis Naohiro Nishida Roberta Gafà Jian Song Zhiyi Guo Cristina Ivan Elisa Barbarotto Ingrid De Vries Xinna Zhang Manuela Ferracin Mike Churchman Janneke F. van Galen Berna H. Beverloo Maryam Shariati Franziska Haderk Marcos R. Estecio Guillermo Garcia-Manero Gijs A. Patijn David C. Gotley Vikas Bhardwaj Imad Shureiqi Subrata Sen Asha S. Multani James Welsh Ken Yamamoto Itsuki Taniguchi Min-Ae Song Steven Gallinger Graham Casey Stephen N. Thibodeau Loïc Le Marchand Maarit Tiirikainen Sendurai A. Mani Wei Zhang Ramana V. Davuluri Koshi Mimori Masaki Mori Anieta M. Sieuwerts John W.M. Martens Ian Tomlinson Massimo Negrini Ioana Berindan-Neagoe John A. Foekens Stanley R. Hamilton
    ...[+44 authors]...,
    Giovanni Lanza
    Scott Kopetz
    Riccardo Fodde
    George A. Calin
    First Published June 24, 2013
  - Enhancement of microhomology-mediated genomic rearrangements by transient loss of mouse Bloom syndrome helicase
    Ayako Yamanishi
    Kosuke Yusa
    Kyoji Horie
    Masahiro Tokunaga
    Kohji Kusano
    Chikara Kokubu
    Junji Takeda
    First Published August 1, 2013
  - The Y chromosome as a regulatory element shaping immune cell transcriptomes and susceptibility to autoimmune disease
    Laure K. Case
    Emma H. Wall
    Julie A. Dragon
    Naresha Saligrama
    Dimitry N. Krementsov
    Mohamad Moussawi
    ...[+1 authors]...,
    James F. Zachary
    Sally A. Huber
    Elizabeth P. Blankenhorn
    Cory Teuscher
    First Published June 25, 2013
  - Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution
    Gang Li
    Brian W. Davis
    Terje Raudsepp
    Alison J. Pearks Wilkerson
    Victor C. Mason
    Malcolm Ferguson-Smith
    Patricia C. O'Brien
    Paul D. Waters
    William J. Murphy
    First Published June 20, 2013
  - Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast
    Daniel A. Skelly
    Gennifer E. Merrihew
    Michael Riffle
    Caitlin F. Connelly
    Emily O. Kerr
    Marnie Johansson Daniel Jaschob Beth Graczyk Nicholas J. Shulman Jon Wakefield Sara J. Cooper Stanley Fields William S. Noble Eric G.D. Muller
    ...[+9 authors]...,
    Trisha N. Davis
    Maitreya J. Dunham
    Michael J. MacCoss
    Joshua M. Akey
    First Published May 29, 2013
  - HIV infection reveals widespread expansion of novel centromeric human endogenous retroviruses
    Rafael Contreras-Galindo
    Mark H. Kaplan
    Shirley He
    Angie C. Contreras-Galindo
    Marta J. Gonzalez-Hernandez
    Ferdinand Kappes Derek Dube Susana M. Chan Dan Robinson Fan Meng Manhong Dai
    ...[+6 authors]...,
    Scott D. Gitlin
    Arul M. Chinnaiyan
    Gilbert S. Omenn
    David M. Markovitz
    First Published May 8, 2013
Methods
- - Estimating and interpreting FST: The impact of rare variants
    Gaurav Bhatia
    Nick Patterson
    Sriram Sankararaman
    Alkes L. Price
    First Published July 16, 2013
  - Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
    Bo Zhang
    Yan Zhou
    Nan Lin
    Rebecca F. Lowdon
    Chibo Hong
    Raman P. Nagarajan Jeffrey B. Cheng Daofeng Li Michael Stevens Hyung Joo Lee Xiaoyun Xing Jia Zhou Vasavi Sundaram GiNell Elliott Junchen Gu Taoping Shi Philippe Gascard Mahvash Sigaroudinia Thea D. Tlsty Theresa Kadlecek Arthur Weiss Henriette O’Geen Peggy J. Farnham Cécile L. Maire Keith L. Ligon Pamela A.F. Madden Angela Tam Richard Moore Martin Hirst
    ...[+24 authors]...,
    Marco A. Marra
    Baoxue Zhang
    Joseph F. Costello
    Ting Wang
    First Published June 26, 2013
  - Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods
    Michael Stevens
    Jeffrey B. Cheng
    Daofeng Li
    Mingchao Xie
    Chibo Hong
    Cécile L. Maire Keith L. Ligon
    ...[+2 authors]...,
    Martin Hirst
    Marco A. Marra
    Joseph F. Costello
    Ting Wang
    First Published June 26, 2013
Resource
- - Cell-type, allelic, and genetic signatures in the human pancreatic beta cell transcriptome
    Alexandra C. Nica
    Halit Ongen
    Jean-Claude Irminger
    Domenico Bosco
    Thierry Berney
    Stylianos E. Antonarakis
    Philippe A. Halban
    Emmanouil T. Dermitzakis
    First Published May 28, 2013

Table of Contents

Volume 23, Issue 9 | September 2013

Research

DNA methylation contributes to natural human variation

Evolution and diversity of copy number variation in the great ape lineage

Deletions of recessive disease genes: CNV contribution to carrier states and disease-causing alleles

NAHR-mediated copy-number variants in a clinical population: Mechanistic insights into both genomic disorders and Mendelizing traits

The complex SNP and CNV genetic architecture of the increased risk of congenital heart defects in Down syndrome

Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma

Next-generation sequencing of paired tyrosine kinase inhibitor-sensitive and -resistant EGFR mutant lung cancer cell lines identifies spectrum of DNA changes associated with drug resistance

CCAT2, a novel noncoding RNA mapping to 8q24, underlies metastatic progression and chromosomal instability in colon cancer

Enhancement of microhomology-mediated genomic rearrangements by transient loss of mouse Bloom syndrome helicase

The Y chromosome as a regulatory element shaping immune cell transcriptomes and susceptibility to autoimmune disease

Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution

Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast

HIV infection reveals widespread expansion of novel centromeric human endogenous retroviruses

Methods

Estimating and interpreting FST: The impact of rare variants

Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm

Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods

Resource

Cell-type, allelic, and genetic signatures in the human pancreatic beta cell transcriptome

Table of Contents

Volume 23, Issue 9 | September 2013

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Research

Methods

Resource