In the name of the father: surnames and genetics
TL;DR: Recent studies involving Y-chromosomal haplotyping and surname analysis are promising and indicate that genealogists of the future could be turning to records written in DNA, as well as in paper archives, to solve their problems.
About: This article is published in Trends in Genetics.The article was published on 2001-06-01. It has received 191 citations till now. The article focuses on the topics: Patronymic surname.
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01 Jan 2015
TL;DR: Until recently, the Y chromosome seemed to fulfill the role of juvenile delinquent among human chromosomes – rich in junk, poor in useful attributes, reluctant to socialize with its neighbors and with an inescapable tendency to degenerate.
Abstract: Until recently, the Y chromosome seemed to fulfill the role of juvenile delinquent among human chromosomes – rich in junk, poor in useful attributes, reluctant to socialize with its neighbors and with an inescapable tendency to degenerate…
5 citations
TL;DR: Zhang et al. as discussed by the authors used a unique dataset of long-run migration in China to provide new measures of cultural distance based on biological evidence, and examined the effect of cultural distances on migration from the Song Dynasty until the twentieth century.
Abstract: This paper uses a unique dataset of long-run migration in China to provide new measures of cultural distance based on biological evidence. We utilise this information to examine the effect of cultural distance on migration in China from the Song Dynasty until the twentieth century. Our findings show that culture has strong effects on migration between regions when controlling for other socio-economic and geographical factors. Population flow is greater where there are fewer cultural differences. This finding not only provides quantitative empirical evidence on linking cultural distance and migration but also leads to a better understanding of the mechanisms resulting in migration for much of China's history.
5 citations
01 Jan 2006
TL;DR: La utilidad del analisis de origen y distribucion geografica-historica de nombres y apellidos para el estudio de migraciones y estructura of the poblacion islámica es pretende demostrar.
5 citations
Journal Article•
TL;DR: In this article, the authors demostrar la utilidad del analisis de origen y distribucion geografica-historica de nombres and apellidos for el estudio de migraciones and estructura de la poblacion, tomando como ejemplo el caso de Mexico.
Abstract: El presente articulo pretende demostrar la utilidad del analisis de origen y distribucion geografica-historica de nombres y apellidos para el estudio de migraciones y estructura de la poblacion, tomando como ejemplo el caso de Mexico. Con diversos listados de apellidos frecuentes de distintos paises, todos ellos procesados en una base de datos relacional y en un sistema de informacion gografica, se logro delimitar regiones y grupos culturales o sociales, que pueden ser parcialmente desentranados mediante el analisis de la distribucion de frecuencias de apellidos. No obstante, es necesario llevar a cabo un analisis mas profundo con un mayor numero de apellidos y un metodo formal de clasificacion, que puede incluir clases socioeconomicas, para agotar la validacion del metodo propuesto.
5 citations
24 Oct 2016
TL;DR: This short tutorial will help computer scientists better understand the privacy and security challenges in today's genomic era and present the high level descriptions of the proposed solutions to protect the privacy of genomic data.
Abstract: With the help of rapidly developing technology, DNA sequencing is becoming less expensive. As a consequence, the research in genomics has gained speed in paving the way to personalized (genomic) medicine, and geneticists need large collections of human genomes to further increase this speed. Furthermore, individuals are using their genomes to learn about their (genetic) predispositions to diseases, their ancestries, and even their (genetic) compatibilities with potential partners. This trend has also caused the launch of health-related websites and online social networks (OSNs), in which individuals share their genomic data (e.g., OpenSNP or 23andMe). On the other hand, genomic data carries much sensitive information about its owner. By analyzing the DNA of an individual, it is now possible to learn about his disease predispositions (e.g., for Alzheimer's or Parkinson's), ancestries, and physical attributes. The threat to genomic privacy is magnified by the fact that a person's genome is correlated to his family members' genomes, thus leading to interdependent privacy risks. This short tutorial will help computer scientists better understand the privacy and security challenges in today's genomic era. We will first highlight the significance of genomic data and the threats for genomic privacy. Then, we will present the high level descriptions of the proposed solutions to protect the privacy of genomic data and we will discuss future research directions. No prerequisite knowledge on biology or genomics is required for the attendees of this proposal. We only require the attendees to have a slight background on cryptography and statistics.
5 citations
Cites background from "In the name of the father: surnames..."
...This information has been applied for instance to track an individual’s ancestral heritage and determine the extent to which individuals with the same surname are related with respect to their genomic variance [Jobling, 2001]....
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References
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TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
Abstract: The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.
22,269 citations
TL;DR: Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems are indicated.
Abstract: A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.
12,098 citations
TL;DR: A method for constructing networks from recombination-free population data that combines features of Kruskal's algorithm for finding minimum spanning trees by favoring short connections, and Farris's maximum-parsimony (MP) heuristic algorithm, which sequentially adds new vertices called "median vectors", except that the MJ method does not resolve ties.
Abstract: Reconstructing phylogenies from intraspecific data (such as human mitochondrial DNA variation) is often a challenging task because of large sample sizes and small genetic distances between individuals. The resulting multitude of plausible trees is best expressed by a network which displays alternative potential evolutionary paths in the form of cycles. We present a method ("median joining" [MJ]) for constructing networks from recombination-free population data that combines features of Kruskal's algorithm for finding minimum spanning trees by favoring short connections, and Farris's maximum-parsimony (MP) heuristic algorithm, which sequentially adds new vertices called "median vectors", except that our MJ method does not resolve ties. The MJ method is hence closely related to the earlier approach of Foulds, Hendy, and Penny for estimating MP trees but can be adjusted to the level of homoplasy by setting a parameter epsilon. Unlike our earlier reduced median (RM) network method, MJ is applicable to multistate characters (e.g., amino acid sequences). An additional feature is the speed of the implemented algorithm: a sample of 800 worldwide mtDNA hypervariable segment I sequences requires less than 3 h on a Pentium 120 PC. The MJ method is demonstrated on a Tibetan mitochondrial DNA RFLP data set.
9,937 citations
TL;DR: A new algorithm for finding tandem repeats which works without the need to specify either the pattern or pattern size is presented and its ability to detect tandem repeats that have undergone extensive mutational change is demonstrated.
Abstract: A tandem repeat in DNA is two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats have been shown to cause human disease, may play a variety of regulatory and evolutionary roles and are important laboratory and analytic tools. Extensive knowledge about pattern size, copy number, mutational history, etc. for tandem repeats has been limited by the inability to easily detect them in genomic sequence data. In this paper, we present a new algorithm for finding tandem repeats which works without the need to specify either the pattern or pattern size. We model tandem repeats by percent identity and frequency of indels between adjacent pattern copies and use statistically based recognition criteria. We demonstrate the algorithm’s speed and its ability to detect tandem repeats that have undergone extensive mutational change by analyzing four sequences: the human frataxin gene, the human β T cell receptor locus sequence and two yeast chromosomes. These sequences range in size from 3 kb up to 700 kb. A World Wide Web server interface at c3.biomath.mssm.edu/trf.html has been established for automated use of the program.
6,577 citations
TL;DR: This book aims to provide a history of Chinese modern art from 17th Century to the present day through the lens of 20th Century critics, practitioners, journalists, and mediaeval and modern-day critics.
Abstract: J. Craig Venter,* Mark D. Adams, Eugene W. Myers, Peter W. Li, Richard J. Mural, Granger G. Sutton, Hamilton O. Smith, Mark Yandell, Cheryl A. Evans, Robert A. Holt, Jeannine D. Gocayne, Peter Amanatides, Richard M. Ballew, Daniel H. Huson, Jennifer Russo Wortman, Qing Zhang, Chinnappa D. Kodira, Xiangqun H. Zheng, Lin Chen, Marian Skupski, Gangadharan Subramanian, Paul D. Thomas, Jinghui Zhang, George L. Gabor Miklos, Catherine Nelson, Samuel Broder, Andrew G. Clark, Joe Nadeau, Victor A. McKusick, Norton Zinder, Arnold J. Levine, Richard J. Roberts, Mel Simon, Carolyn Slayman, Michael Hunkapiller, Randall Bolanos, Arthur Delcher, Ian Dew, Daniel Fasulo, Michael Flanigan, Liliana Florea, Aaron Halpern, Sridhar Hannenhalli, Saul Kravitz, Samuel Levy, Clark Mobarry, Knut Reinert, Karin Remington, Jane Abu-Threideh, Ellen Beasley, Kendra Biddick, Vivien Bonazzi, Rhonda Brandon, Michele Cargill, Ishwar Chandramouliswaran, Rosane Charlab, Kabir Chaturvedi, Zuoming Deng, Valentina Di Francesco, Patrick Dunn, Karen Eilbeck, Carlos Evangelista, Andrei E. Gabrielian, Weiniu Gan, Wangmao Ge, Fangcheng Gong, Zhiping Gu, Ping Guan, Thomas J. Heiman, Maureen E. Higgins, Rui-Ru Ji, Zhaoxi Ke, Karen A. Ketchum, Zhongwu Lai, Yiding Lei, Zhenya Li, Jiayin Li, Yong Liang, Xiaoying Lin, Fu Lu, Gennady V. Merkulov, Natalia Milshina, Helen M. Moore, Ashwinikumar K Naik, Vaibhav A. Narayan, Beena Neelam, Deborah Nusskern, Douglas B. Rusch, Steven Salzberg, Wei Shao, Bixiong Shue, Jingtao Sun, Zhen Yuan Wang, Aihui Wang, Xin Wang, Jian Wang, Ming-Hui Wei, Ron Wides, Chunlin Xiao, Chunhua Yan, Alison Yao, Jane Ye, Ming Zhan, Weiqing Zhang, Hongyu Zhang, Qi Zhao, Liansheng Zheng, Fei Zhong, Wenyan Zhong, Shiaoping C. Zhu, Shaying Zhao, Dennis Gilbert, Suzanna Baumhueter, Gene Spier, Christine Carter, Anibal Cravchik, Trevor Woodage, Feroze Ali, Huijin An, Aderonke Awe, Danita Baldwin, Holly Baden, Mary Barnstead, Ian Barrow, Karen Beeson, Dana Busam, Amy Carver, Angela Center, Ming Lai Cheng, Liz Curry, Steve Danaher, Lionel Davenport, Raymond Desilets, Susanne Dietz, Kristina Dodson, Lisa Doup, Steven Ferriera, Neha Garg, Andres Gluecksmann, Brit Hart, Jason Haynes, Charles Haynes, Cheryl Heiner, Suzanne Hladun, Damon Hostin, Jarrett Houck, Timothy Howland, Chinyere Ibegwam, Jeffery Johnson, Francis Kalush, Lesley Kline, Shashi Koduru, Amy Love, Felecia Mann, David May, Steven McCawley, Tina McIntosh, Ivy McMullen, Mee Moy, Linda Moy, Brian Murphy, Keith Nelson, Cynthia Pfannkoch, Eric Pratts, Vinita Puri, Hina Qureshi, Matthew Reardon, Robert Rodriguez, Yu-Hui Rogers, Deanna Romblad, Bob Ruhfel, Richard Scott, Cynthia Sitter, Michelle Smallwood, Erin Stewart, Renee Strong, Ellen Suh, Reginald Thomas, Ni Ni Tint, Sukyee Tse, Claire Vech, Gary Wang, Jeremy Wetter, Sherita Williams, Monica Williams, Sandra Windsor, Emily Winn-Deen, Keriellen Wolfe, Jayshree Zaveri, Karena Zaveri, Josep F. Abril, Roderic Guigó, Michael J. Campbell, Kimmen V. Sjolander, Brian Karlak, Anish Kejariwal, Huaiyu Mi, Betty Lazareva, Thomas Hatton, Apurva Narechania, Karen Diemer, Anushya Muruganujan, Nan Guo, Shinji Sato, Vineet Bafna, Sorin Istrail, Ross Lippert, Russell Schwartz, Brian Walenz, Shibu Yooseph, David Allen, Anand Basu, James Baxendale, Louis Blick, Marcelo Caminha, John Carnes-Stine, Parris Caulk, Yen-Hui Chiang, My Coyne, Carl Dahlke, Anne Deslattes Mays, Maria Dombroski, Michael Donnelly, Dale Ely, Shiva Esparham, Carl Fosler, Harold Gire, Stephen Glanowski, Kenneth Glasser, Anna Glodek, Mark Gorokhov, Ken Graham, Barry Gropman, Michael Harris, Jeremy Heil, Scott Henderson, Jeffrey Hoover, Donald Jennings, Catherine Jordan, James Jordan, John Kasha, Leonid Kagan, Cheryl Kraft, Alexander Levitsky, Mark Lewis, Xiangjun Liu, John Lopez, Daniel Ma, William Majoros, Joe McDaniel, Sean Murphy, Matthew Newman, Trung Nguyen, Ngoc Nguyen, Marc Nodell, Sue Pan, Jim Peck, Marshall Peterson, William Rowe, Robert Sanders, John Scott, Michael Simpson, Thomas Smith, Arlan Sprague, Timothy Stockwell, Russell Turner, Eli Venter, Mei Wang, Meiyuan Wen, David Wu, Mitchell Wu, Ashley Xia, Ali Zandieh, Xiaohong Zhu T H E H U M A N G E N O M E
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