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Lo CL, Shen F, Baumgarner K, Cramer MJ, Lossie AC. Identification of 129S6/SvEvTac-specific polymorphisms on mouse chromosome 11. DNA Cell Biol 2011; 31:402-14. [PMID: 21988490 DOI: 10.1089/dna.2011.1353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Polymorphisms such as single-nucleotide polymorphisms (SNPs) and insertions/deletions (Indels) can be associated with phenotypic traits and be used as markers for disease diagnosis. Identification of these genetic variations within laboratory mice is crucial to improve our understanding of the genetic background of the mice used for research. As part of a positional cloning project, we sequenced six genes (Mettl16, Evi2a, Psmd11, Cct6d, Rffl, and Ap2b1) within a 6.8-Mb domain of mmu chr 11 in the C57BL/6J and 129S6/SvEvTac inbred strains. Although 129S6/SvEvTac is widely used in the mouse community, there is very little current (or projected future) sequence information available for this strain. We identified 6 Indels and 21 novel SNPs and confirmed genotype information for 114 additional SNPs in these 6 genes. Mettl16 and Ap2b1 contained the largest numbers of variants between the C57BL/6J and 129S6/SvEvTac strains. In addition, we found five new SNPs between 129S6/SvEvTac and 129S1/SvImJ within the Ap2b1 locus. Although we did not detect differences between C57BL/6J and 129S6/SvEvTac within Evi2a, this locus contains a relatively high SNP density compared with the surrounding sequence. Our study highlights the genetic differences among three inbred mouse strains (C57BL/6J, 129S6/SvEvTac, and 129S1/SvImJ) and provides valuable sequence information that can be used to track alleles in genomics-based studies.
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Affiliation(s)
- Chiao-Ling Lo
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana 47907, USA
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Liu WW, Gao YX, Zhou LP, Duan A, Tan LL, Li WZ, Yan M, Yang HY, Yan SL, Wang MQ, Ding WJ. Observations on Copy Number Variations in a Kidney-yang Deficiency Syndrome Family. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2011; 2011:548358. [PMID: 21811512 PMCID: PMC3136678 DOI: 10.1093/ecam/neq069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Accepted: 05/19/2010] [Indexed: 11/17/2022]
Abstract
We have performed an analysis of a family with kidney-yang deficiency syndrome (KDS) in order to determine the structural genomic variations through a novel approach designated as “copy number variants” (CNVs). Twelve KDS subjects and three healthy spouses from this family were included in this study. Genomic DNA samples were genotyped utilizing an Affymetrix 100 K single nucleotide polymorphism array, and CNVs were identified by Copy Number Algorithm (CNAT4.0, Affymetrix). Our results demonstrate that 447 deleted and 476 duplicated CNVs are shared among KDS subjects within the family. The homologus ratio of deleted CNVs was as high as 99.78%. One-copy-duplicated CNVs display mid-range homology. For two copies of duplicated CNVs (CNV4), a markedly heterologous ratio was observed. Therefore, with the important exception of CNV4, our data shows that CNVs shared among KDS subjects display typical Mendelian inheritance. A total of 113 genes with established functions were identified from the CNV flanks; significantly enriched genes surrounding CNVs may contribute to certain adaptive benefit. These genes could be classified into categories including: binding and transporter, cell cycle, signal transduction, biogenesis, nerve development, metabolism regulation and immune response. They can also be included into three pathways, that is, signal transduction, metabolic processes and immunological networks. Particularly, the results reported here are consistent with the extensive impairments observed in KDS patients, involving the mass-energy-information-carrying network. In conclusion, this article provides the first set of CNVs from KDS patients that will facilitate our further understanding of the genetic basis of KDS and will allow novel strategies for a rational therapy of this disease.
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Affiliation(s)
- Wei Wei Liu
- Department of Fundamental Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China
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Koboldt DC, Miller RD. Identification of Polymorphic Markers for Genetic Mapping. Genomics 2010. [DOI: 10.1002/9780470711675.ch2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Atanur SS, Birol I, Guryev V, Hirst M, Hummel O, Morrissey C, Behmoaras J, Fernandez-Suarez XM, Johnson MD, McLaren WM, Patone G, Petretto E, Plessy C, Rockland KS, Rockland C, Saar K, Zhao Y, Carninci P, Flicek P, Kurtz T, Cuppen E, Pravenec M, Hubner N, Jones SJM, Birney E, Aitman TJ. The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance. Genome Res 2010; 20:791-803. [PMID: 20430781 DOI: 10.1101/gr.103499.109] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The spontaneously hypertensive rat (SHR) is the most widely studied animal model of hypertension. Scores of SHR quantitative loci (QTLs) have been mapped for hypertension and other phenotypes. We have sequenced the SHR/OlaIpcv genome at 10.7-fold coverage by paired-end sequencing on the Illumina platform. We identified 3.6 million high-quality single nucleotide polymorphisms (SNPs) between the SHR/OlaIpcv and Brown Norway (BN) reference genome, with a high rate of validation (sensitivity 96.3%-98.0% and specificity 99%-100%). We also identified 343,243 short indels between the SHR/OlaIpcv and reference genomes. These SNPs and indels resulted in 161 gain or loss of stop codons and 629 frameshifts compared with the BN reference sequence. We also identified 13,438 larger deletions that result in complete or partial absence of 107 genes in the SHR/OlaIpcv genome compared with the BN reference and 588 copy number variants (CNVs) that overlap with the gene regions of 688 genes. Genomic regions containing genes whose expression had been previously mapped as cis-regulated expression quantitative trait loci (eQTLs) were significantly enriched with SNPs, short indels, and larger deletions, suggesting that some of these variants have functional effects on gene expression. Genes that were affected by major alterations in their coding sequence were highly enriched for genes related to ion transport, transport, and plasma membrane localization, providing insights into the likely molecular and cellular basis of hypertension and other phenotypes specific to the SHR strain. This near complete catalog of genomic differences between two extensively studied rat strains provides the starting point for complete elucidation, at the molecular level, of the physiological and pathophysiological phenotypic differences between individuals from these strains.
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Affiliation(s)
- Santosh S Atanur
- Physiological Genomics and Medicine Group, Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London W12 0NN, United Kingdom
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Abstract
Biomedical researchers studying gene function should consider the impact of variation, even if genetics is not the primary objective of an investigation. Information on genetic variation can provide a valuable insight into the functional range and critical regions of a gene, protein or regulatory element. Genetic variants may be diverse in nature, ranging from single nucleotide variants, tandem repeats, small insertions or deletions to large copy number variants. Until recently, information on genetic variation was quite limited, but now a range of large scale surveys of variation have made plentiful data on common variation and a picture is beginning to emerge from the driving forces in human evolution and population diversification. Next-generation sequencing technologies are moving knowledge into a new phase focused on the individual genome and complete disclosure of individual variation, including the rarest of variants. The consequences of these advances in medicine are unresolved, but it is clear that biomedical researchers cannot afford to ignore this information. This review presents a broad overview of the in silico methods that will allow a researcher to quickly review known variation in a gene of interest, providing some pointers for further investigation.
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Ding WJ, Zeng YZ, Li WH, Zhang TE, Liu WW, Teng XK, Ma YX, Yan SL, Wan JMF, Wang MQ. Identification of Linkage Disequilibrium SNPs from a Kidney-Yang Deficiency Syndrome Pedigree. THE AMERICAN JOURNAL OF CHINESE MEDICINE 2009; 37:427-38. [PMID: 19606505 DOI: 10.1142/s0192415x09006953] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In order to probe the genetic traits of Kidney-yang Deficiency Syndrome (KDS), we employed a national standard of KDS diagnosis for the collection of KDS subjects. Each candidate KDS subject from a typical family was diagnosed by 5 independent physicians of Traditional Chinese Medicine (TCM), and repeated for 3 years, all on the first Saturday of December. Fifteen samples of genomic DNA were isolated and genotyped by Affymetrix 100 K arrays of single nucleotide polymorphism (SNP). Then appropriate tools were used for the analysis of linkage disequilibrium (LD) and bioinformatic mining of LD SNPs. The results indicated that our procedure of TCM diagnosis can effectively collect KDS subjects and therefore provide substantial basis for the linkage analysis of KDS. Five SNPs (i.e. rs514207, rs1054020, rs7685923, rs10515889 and rs10516202) were identified as LD SNPs from this KDS family, representing an unprecedented set of LD SNPs derived from TCM syndrome. These SNPs demonstrate midrange linkage disequilibrium within the KDS family. Two genes with established functions were identified within 100 bp of these SNPs. One is Homo sapiens double cortin domain containing 5, which interacts selectively with mono-, di- or tri-saccharide carbohydrate and involves certain signaling cascades. Another one, leucyl-tRNA synthetase, is also a pleiotropic gene response to cysteinyl-tRNA aminoacylation and protein biosynthesis. In conclusion, KDS is involved in special SNP linkage disequilibrium in the intragenic level, and genes within the flanks of these SNPs suggest some essential symptoms of KDS. However, definitive evidence to confirm or exclude these loci and to establish their biological activities will be required.
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Affiliation(s)
- Wei Jun Ding
- Department of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China.
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7
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Daniel R, Walsh SJ. The Continuing Evolution of Forensic DNA Profiling - From STRS to SNPS. AUST J FORENSIC SCI 2006. [DOI: 10.1080/00450610609410633] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Kofiadi IA, Rebrikov DV. Methods for detecting single nucleotide polymorphisms: Allele-specific PCR and hybridization with oligonucleotide probe. RUSS J GENET+ 2006. [DOI: 10.1134/s1022795406010029] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Miller RD, Phillips MS, Jo I, Donaldson MA, Studebaker JF, Addleman N, Alfisi SV, Ankener WM, Bhatti HA, Callahan CE, Carey BJ, Conley CL, Cyr JM, Derohannessian V, Donaldson RA, Elosua C, Ford SE, Forman AM, Gelfand CA, Grecco NM, Gutendorf SM, Hock CR, Hozza MJ, Hur S, In SM, Jackson DL, Jo SA, Jung SC, Kim S, Kimm K, Kloss EF, Koboldt DC, Kuebler JM, Kuo FS, Lathrop JA, Lee JK, Leis KL, Livingston SA, Lovins EG, Lundy ML, Maggan S, Minton M, Mockler MA, Morris DW, Nachtman EP, Oh B, Park C, Park CW, Pavelka N, Perkins AB, Restine SL, Sachidanandam R, Reinhart AJ, Scott KE, Shah GJ, Tate JM, Varde SA, Walters A, White JR, Yoo YK, Lee JE, Boyce-Jacino MT, Kwok PY. High-density single-nucleotide polymorphism maps of the human genome. Genomics 2005; 86:117-26. [PMID: 15961272 PMCID: PMC1885222 DOI: 10.1016/j.ygeno.2005.04.012] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2004] [Revised: 03/30/2005] [Accepted: 04/16/2005] [Indexed: 11/17/2022]
Abstract
Here we report a large, extensively characterized set of single-nucleotide polymorphisms (SNPs) covering the human genome. We determined the allele frequencies of 55,018 SNPs in African Americans, Asians (Japanese-Chinese), and European Americans as part of The SNP Consortium's Allele Frequency Project. A subset of 8333 SNPs was also characterized in Koreans. Because these SNPs were ascertained in the same way, the data set is particularly useful for modeling. Our results document that much genetic variation is shared among populations. For autosomes, some 44% of these SNPs have a minor allele frequency > or =10% in each population, and the average allele frequency differences between populations with different continental origins are less than 19%. However, the several percentage point allele frequency differences among the closely related Korean, Japanese, and Chinese populations suggest caution in using mixtures of well-established populations for case-control genetic studies of complex traits. We estimate that approximately 7% of these SNPs are private SNPs with minor allele frequencies <1%. A useful set of characterized SNPs with large allele frequency differences between populations (>60%) can be used for admixture studies. High-density maps of high-quality, characterized SNPs produced by this project are freely available.
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Affiliation(s)
| | | | - Inho Jo
- Department of Biomedical Sciences, National Institute of Health, Seoul, South Korea
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Soyoung Hur
- Department of Biomedical Sciences, National Institute of Health, Seoul, South Korea
| | | | | | - Sangmee Ahn Jo
- Department of Biomedical Sciences, National Institute of Health, Seoul, South Korea
| | - Sung-Chul Jung
- Department of Biomedical Sciences, National Institute of Health, Seoul, South Korea
| | - Sook Kim
- DNA Link, Inc., Seoul, South Korea
| | - Kuchan Kimm
- National Genome Research Institute, National Institute of Health, Seoul, South Korea
| | - Ellen F. Kloss
- Washington University, Division of Dermatology, St. Louis, MO, USA
| | | | | | | | | | - Jong-Keuk Lee
- National Genome Research Institute, National Institute of Health, Seoul, South Korea
| | | | | | | | | | - Sima Maggan
- Orchid BioSciences, Inc., Princeton, NJ, USA
| | - Matthew Minton
- Washington University, Division of Dermatology, St. Louis, MO, USA
| | | | | | | | - Bermseok Oh
- National Genome Research Institute, National Institute of Health, Seoul, South Korea
| | - Chan Park
- National Genome Research Institute, National Institute of Health, Seoul, South Korea
| | | | - Nicholas Pavelka
- Washington University, Division of Dermatology, St. Louis, MO, USA
| | | | | | | | | | | | | | | | | | - Amy Walters
- Orchid BioSciences, Inc., Princeton, NJ, USA
| | | | | | - Jong-Eun Lee
- DNA Link, Inc., Seoul, South Korea
- *Corresponding authors. Jong-Eun Lee is to be contacted at fax: +82 2 364 4778. Michael T. Boyce-Jacino, fax: +1 609 818 0054. Pui-Yan Kwok, fax: +1 415 476 2956. E-mail addresses: (J.-E. Lee), (M.T. Boyce-Jacinto), (P.-Y. Kwok)
| | - Michael T. Boyce-Jacino
- Orchid BioSciences, Inc., Princeton, NJ, USA
- *Corresponding authors. Jong-Eun Lee is to be contacted at fax: +82 2 364 4778. Michael T. Boyce-Jacino, fax: +1 609 818 0054. Pui-Yan Kwok, fax: +1 415 476 2956. E-mail addresses: (J.-E. Lee), (M.T. Boyce-Jacinto), (P.-Y. Kwok)
| | - Pui-Yan Kwok
- Washington University, Division of Dermatology, St. Louis, MO, USA
- *Corresponding authors. Jong-Eun Lee is to be contacted at fax: +82 2 364 4778. Michael T. Boyce-Jacino, fax: +1 609 818 0054. Pui-Yan Kwok, fax: +1 415 476 2956. E-mail addresses: (J.-E. Lee), (M.T. Boyce-Jacinto), (P.-Y. Kwok)
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Jansson M, McCarthy S, Sullivan PF, Dickman P, Andersson B, Oreland L, Schalling M, Pedersen NL. MAOA haplotypes associated with thrombocyte-MAO activity. BMC Genet 2005; 6:46. [PMID: 16174289 PMCID: PMC1249565 DOI: 10.1186/1471-2156-6-46] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2005] [Accepted: 09/20/2005] [Indexed: 11/10/2022] Open
Abstract
Background The aim was to ascertain whether thrombocyte MAO (trbc-MAO) activity and depressed state are genetically associated with the MAO locus on chromosome X (Xp11.3 – 11.4). We performed novel sequencing of the MAO locus and validated genetic variants found in public databases prior to constructing haplotypes of the MAO locus in a Swedish sample (N = 573 individuals). Results Our results reveal a profound SNP desert in the MAOB gene. Both the MAOA and MAOB genes segregate as two distinct LD blocks. We found a significant association between two MAOA gene haplotypes and reduced trbc-MAO activity, but no association with depressed state. Conclusion The MAO locus seems to have an effect on trbc-MAO activity in the study population. The findings suggest incomplete X-chromosome inactivation at this locus. It is plausible that a gene-dosage effect can provide some insight into the greater prevalence of depressed state in females than males.
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Affiliation(s)
- Mårten Jansson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Shane McCarthy
- Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden
| | - Patrick F Sullivan
- Departments of Genetics, Psychiatry & Epidemiology, University of North Carolina at Chapel Hill, NC, USA
| | - Paul Dickman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Björn Andersson
- Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden
| | - Lars Oreland
- Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Martin Schalling
- Department of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Psychology, University of Southern California, Los Angeles, USA
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11
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Hagelin J. The Use of Live Apes in Research in the Twenty-first Century. Altern Lab Anim 2005; 33:111-8. [PMID: 16180986 DOI: 10.1177/026119290503300206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A literature-based survey was conducted on the use of live apes in research between 2000 and 2003. The 599 studies identified and considered were grouped according to area of research, taxonomy and geographic location of the work. The results suggested that behaviour/cognition, conservation and various applications related to virology (most notably, hepatitis and HIV) were the most frequent areas of research. Of the studies, 73% were classified as non-invasive, whereas 27% were classified as invasive. Among the invasive studies, 39% were scored as of mild severity, and 61% were scored as of moderate/substantial severity. Pan species were involved in 65% of the studies, Gorilla species in 15%, Pongo species in 12%, and Hylobates species in 8%. Most of the invasive research was conducted in the USA (60%). The majority of the non-invasive research was conducted in the USA (31%), Japan (13%), or in the animals’ natural habitats in Africa (35%) and Asia (8%).
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12
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Bhangale TR, Rieder MJ, Livingston RJ, Nickerson DA. Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes. Hum Mol Genet 2004; 14:59-69. [PMID: 15525656 DOI: 10.1093/hmg/ddi006] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Despite being the second most frequent type of polymorphism in the genome, diallelic insertion-deletion polymorphisms (indels) have received far less attention in the study of sequence variation. In this report, we describe an approach that can detect indels in the heterozygous state and can comprehensively identify indels in the target sequence. Using this approach, we identified 2393 indels in a set of 330 candidate genes, i.e. an average of seven indels per gene with about two indels per gene being common (minor allele frequency >or=0.1). We compared the population genetic characteristics of indels with substitutions in this data. Our data supported the findings that deletions occur more frequently in the human genome. 5'-UTR and coding regions of the genes showed a significantly lower diversity for indels compared with other regions, suggesting differences in effects of selection on indels and substitutions. Sequence diversity and pairwise linkage disequilibrium (LD) findings of the different populations were similar to earlier results and included a greater skew towards low-frequency variants and a faster rate of LD decay in the African-descent population compared with the non-African populations. Within populations, the allele frequency spectra and LD-decay profiles for indels were similar to substitutions. Overall, the findings suggest that, although the mechanisms giving rise to indels may be different from those causing substitutions, the evolutionary histories of indels and substitutions are similar, and that indels can play a valuable role in association studies and marker selection strategies.
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Affiliation(s)
- Tushar R Bhangale
- Department of Bioengineering, University of Washington, Seattle, WA 98195-7730, USA
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13
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Onouchi Y, Onoue S, Tamari M, Wakui K, Fukushima Y, Yashiro M, Nakamura Y, Yanagawa H, Kishi F, Ouchi K, Terai M, Hamamoto K, Kudo F, Aotsuka H, Sato Y, Nariai A, Kaburagi Y, Miura M, Saji T, Kawasaki T, Nakamura Y, Hata A. CD40 ligand gene and Kawasaki disease. Eur J Hum Genet 2004; 12:1062-8. [PMID: 15367912 DOI: 10.1038/sj.ejhg.5201266] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Kawasaki disease (KD) is an acute systemic vasculitis syndrome of infants and young children. Although its etiology is largely unknown, epidemiological findings suggest that genetic factors play a role in the pathogenesis of KD. To identify genetic factors, affected sib-pair analysis has been performed. One of the identified peaks was located on the Xq26 region. A recent report of elevated expression of CD40 ligand (CD40L), which maps to Xq26, during the acute-phase KD, and its relationship to the development of coronary artery lesions (CAL) prompted us to screen for polymorphism of CD40L and to study the association of the gene to KD. A newly identified SNP in intron 4 (IVS4+121 A>G) is marginally over-represented in KD patients as compared to controls (109/602, 18.1 vs 111/737, 15.1%). When male KD patients with CAL were analyzed as a patient group, the SNP was significantly more frequent than in controls (15/58, 25.9%, vs 111/737, 15.1%, OR=2.0, 95% CI=1.07-3.66; P=0.030). Interestingly, this variation was extremely rare in a control Caucasian population (1/145, 0.7%). Our results suggest a role of CD40L in the pathogenesis of CAL and might explain the excess of males affected with KD.
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Affiliation(s)
- Yoshihiro Onouchi
- Laboratory for Gastrointestinal Diseases, SNP Research Center, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Japan.
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14
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Waterston RH, Hillier LW, Fulton LA, Fulton RS, Graves TA, Pepin KH, Bork P, Suyama M, Torrents D, Chinwalla AT, Mardis ER, McPherson JD, Wilson RK. The human genome: genes, pseudogenes, and variation on chromosome 7. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2004; 68:13-22. [PMID: 15338598 DOI: 10.1101/sqb.2003.68.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- R H Waterston
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
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15
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Affiliation(s)
- Stephen F Schaffner
- Whitehead/MIT Center for Genome Research, Cambridge, Massachusetts 02139, USA.
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Miller RD, Duan S, Lovins EG, Kloss EF, Kwok PY. Efficient high-throughput resequencing of genomic DNA. Genome Res 2003; 13:717-20. [PMID: 12654721 PMCID: PMC430165 DOI: 10.1101/gr.886203] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Targeted resequencing of genomic DNA from organisms such as humans is an important tool enabling experimental access to variation within the species and between similar species. Taking full advantage of the reference genome sequences in designing robust, specific PCR assays and using stringent conditions, resequencing can be done efficiently without purification of the PCR product. By using a 10-fold greater amount of one primer when setting up the PCR initially in a new version of asymmetric PCR, one simply adds the rest of the sequencing reagents at the end of PCR and allows the sequencing reaction to proceed, with the excess PCR primer serving as the sequencing primer. We demonstrated that this streamlined protocol can be used with PCR products up to 1300 bp and had up to a 97% success rate in high-throughput analysis of allele frequencies for >30,000 single-nucleotide polymorphisms (SNPs). SNP primers and characterization results are provided at http://snp.wustl.edu.
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Affiliation(s)
- Raymond D Miller
- Washington University, Division of Dermatology, St. Louis, Missouri 63110, USA
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17
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Marth G, Schuler G, Yeh R, Davenport R, Agarwala R, Church D, Wheelan S, Baker J, Ward M, Kholodov M, Phan L, Czabarka E, Murvai J, Cutler D, Wooding S, Rogers A, Chakravarti A, Harpending HC, Kwok PY, Sherry ST. Sequence variations in the public human genome data reflect a bottlenecked population history. Proc Natl Acad Sci U S A 2003; 100:376-81. [PMID: 12502794 PMCID: PMC140982 DOI: 10.1073/pnas.222673099] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Single-nucleotide polymorphisms (SNPs) constitute the great majority of variations in the human genome, and as heritable variable landmarks they are useful markers for disease mapping and resolving population structure. Redundant coverage in overlaps of large-insert genomic clones, sequenced as part of the Human Genome Project, comprises a quarter of the genome, and it is representative in terms of base compositional and functional sequence features. We mined these regions to produce 500,000 high-confidence SNP candidates as a uniform resource for describing nucleotide diversity and its regional variation within the genome. Distributions of marker density observed at different overlap length scales under a model of recombination and population size change show that the history of the population represented by the public genome sequence is one of collapse followed by a recent phase of mild size recovery. The inferred times of collapse and recovery are Upper Paleolithic, in agreement with archaeological evidence of the initial modern human colonization of Europe.
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Affiliation(s)
- Gabor Marth
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA.
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Weber JL, David D, Heil J, Fan Y, Zhao C, Marth G. Human diallelic insertion/deletion polymorphisms. Am J Hum Genet 2002; 71:854-62. [PMID: 12205564 PMCID: PMC378541 DOI: 10.1086/342727] [Citation(s) in RCA: 245] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2002] [Accepted: 07/09/2002] [Indexed: 12/20/2022] Open
Abstract
We report the identification and characterization of 2,000 human diallelic insertion/deletion polymorphisms (indels) distributed throughout the human genome. Candidate indels were identified by comparison of overlapping genomic or cDNA sequences. Average confirmation rate for indels with a > or =2-nt allele-length difference was 58%, but the confirmation rate for indels with a 1-nt length difference was only 14%. The vast majority of the human diallelic indels were monomorphic in chimpanzees and gorillas. The ratio of deletionrcolon;insertion mutations was 4.1. Allele frequencies for the indels were measured in Europeans, Africans, Japanese, and Native Americans. New alleles were generally lower in frequency than old alleles. This tendency was most pronounced for the Africans, who are likely to be closest among the four groups to the original modern human population. Diallelic indels comprise approximately 8% of all human polymorphisms. Their abundance and ease of analysis make them useful for many applications.
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Affiliation(s)
- James L Weber
- Center for Medical Genetics, Marshfield Medical Research Foundation, Marshfield, WI 54449, USA.
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Sabeti P, Usen S, Farhadian S, Jallow M, Doherty T, Newport M, Pinder M, Ward R, Kwiatkowski D. CD40L association with protection from severe malaria. Genes Immun 2002; 3:286-91. [PMID: 12140747 DOI: 10.1038/sj.gene.6363877] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2001] [Revised: 02/19/2002] [Accepted: 02/19/2002] [Indexed: 11/09/2022]
Abstract
CD40 ligand (CD40L), a glycoprotein involved in B cell proliferation, antigen presenting cell activation, and Ig class switching, is important in the immune response to infection. Rare coding mutations in CD40L can lead to life-threatening immunodeficiency but the potential for common variants to alter disease susceptibility remains to be explored. To identify polymorphisms in CD40L, we sequenced 2.3 kb of the 5' flanking region and the first exon of the gene in DNA samples from 36 Gambian females and one chimpanzee. Diversity was lower than the average reported for other areas of the X chromosome, and only two polymorphisms were identified. The polymorphisms were genotyped in DNA samples from 957 Gambian individuals, cases and controls from a study of severe malaria. A significant reduction in risk for severe malaria (OR = 0.52, P = 0.002) was associated with males hemizygous for the CD40L-726C. Analysis by transmission disequilibrium test of 371 cases, for whom DNA from both parents was also available, confirmed the result was not due to stratification (P = 0.04). A similar but non-significant trend was found in females. This preliminary association of a common variant in CD40L with a malaria resistance phenotype encourages further genetic characterization of the role of CD40L in infectious disease.
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Affiliation(s)
- P Sabeti
- Wellcome Trust Centre for Human Genetics, Oxford, UK
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Aquadro CF, Bauer DuMont V, Reed FA. Genome-wide variation in the human and fruitfly: a comparison. Curr Opin Genet Dev 2001; 11:627-34. [PMID: 11682305 DOI: 10.1016/s0959-437x(00)00245-8] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Average levels of nucleotide diversity are ten-fold lower in humans than in the fruitfly, Drosophila melanogaster. Despite this difference, apparently as a result of a lower population size, patterns of genomic diversity are strikingly similar in being correlated with local rates of recombination, and influenced by similar interactions between positive natural selection and recombination. Both species also show lower levels of variation on average in non-African compared to African populations, reflecting a similar evolutionary history and perhaps both natural selection and founder effects in new environments.
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Affiliation(s)
- C F Aquadro
- Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, New York 14853, USA.
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Lai E. Application of SNP technologies in medicine: lessons learned and future challenges. Genome Res 2001; 11:927-9. [PMID: 11381021 DOI: 10.1101/gr.192301] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- E Lai
- Discovery Genetics, Genetics Research, GlaxoSmithKline, Research Triangle Park, North Carolina 27709, USA.
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