Investigative genetics最新文献

{"title":"Comment on Kokshoorn, B, and Blankers, BJ 'Response to Grisedale, KS and van Daal, A: comparison of STR profiling from low template DNA extracts with and without the consensus profiling method'.","authors":"Kelly Grisedale,&nbsp;Angela van Daal","doi":"10.1186/2041-2223-4-2","DOIUrl":"https://doi.org/10.1186/2041-2223-4-2","url":null,"abstract":"<p><p> Kokshoorn and Blankers responded to our recent article by saying that replicate analysis and consensus profiling of low template samples was best in terms of reliability and objectivity. We agree that the consensus approach has benefits, particularly in eliminating non-repeating spurious alleles from the final profile. However, with the development of statistical models that can accommodate stochastic effects and allele drop in, it may be beneficial to perform a single amplification with three times the amount of template, since much information is lost from the profile using the consensus approach.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":" ","pages":"2"},"PeriodicalIF":0.0,"publicationDate":"2013-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-4-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40207141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The bishop and the actress.","authors":"Mark A Jobling","doi":"10.1186/2041-2223-3-27","DOIUrl":"https://doi.org/10.1186/2041-2223-3-27","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"3 1","pages":"27"},"PeriodicalIF":0.0,"publicationDate":"2012-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-3-27","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31145154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editors' pick: Christmas is coming - time for chocolate to get ready for your Nobel Prize.","authors":"Manfred Kayser","doi":"10.1186/2041-2223-3-26","DOIUrl":"https://doi.org/10.1186/2041-2223-3-26","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"3 1","pages":"26"},"PeriodicalIF":0.0,"publicationDate":"2012-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-3-26","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31115602","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Isolating DNA from sexual assault cases: a comparison of standard methods with a nuclease-based approach.","authors":"Alex M Garvin,&nbsp;Andrea Fischer,&nbsp;Jutta Schnee-Griese,&nbsp;Andrea Jelinski,&nbsp;Michel Bottinelli,&nbsp;Gianni Soldati,&nbsp;Monica Tubio,&nbsp;Vincent Castella,&nbsp;Nathalie Monney,&nbsp;Naseem Malik,&nbsp;Michelle Madrid","doi":"10.1186/2041-2223-3-25","DOIUrl":"https://doi.org/10.1186/2041-2223-3-25","url":null,"abstract":"<p><strong>Unlabelled: </strong></p><p><strong>Background: </strong>Profiling sperm DNA present on vaginal swabs taken from rape victims often contributes to identifying and incarcerating rapists. Large amounts of the victim's epithelial cells contaminate the sperm present on swabs, however, and complicate this process. The standard method for obtaining relatively pure sperm DNA from a vaginal swab is to digest the epithelial cells with Proteinase K in order to solubilize the victim's DNA, and to then physically separate the soluble DNA from the intact sperm by pelleting the sperm, removing the victim's fraction, and repeatedly washing the sperm pellet. An alternative approach that does not require washing steps is to digest with Proteinase K, pellet the sperm, remove the victim's fraction, and then digest the residual victim's DNA with a nuclease.</p><p><strong>Methods: </strong>The nuclease approach has been commercialized in a product, the Erase Sperm Isolation Kit (PTC Labs, Columbia, MO, USA), and five crime laboratories have tested it on semen-spiked female buccal swabs in a direct comparison with their standard methods. Comparisons have also been performed on timed post-coital vaginal swabs and evidence collected from sexual assault cases.</p><p><strong>Results: </strong>For the semen-spiked buccal swabs, Erase outperformed the standard methods in all five laboratories and in most cases was able to provide a clean male profile from buccal swabs spiked with only 1,500 sperm. The vaginal swabs taken after consensual sex and the evidence collected from rape victims showed a similar pattern of Erase providing superior profiles.</p><p><strong>Conclusions: </strong>In all samples tested, STR profiles of the male DNA fractions obtained with Erase were as good as or better than those obtained using the standard methods.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"3 1","pages":"25"},"PeriodicalIF":0.0,"publicationDate":"2012-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-3-25","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31098150","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editors' pick: codeine toxicity prediction in young infants - genotype the mothers.","authors":"Antti Sajantila","doi":"10.1186/2041-2223-3-24","DOIUrl":"https://doi.org/10.1186/2041-2223-3-24","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"3 1","pages":"24"},"PeriodicalIF":0.0,"publicationDate":"2012-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-3-24","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31078614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High diversity and no significant selection signal of human ADH1B gene in Tibet.","authors":"Yan Lu, Longli Kang, Kang Hu, Chuanchao Wang, Xiaoji Sun, Feng Chen, Judith R Kidd, Kenneth K Kidd, Hui Li","doi":"10.1186/2041-2223-3-23","DOIUrl":"10.1186/2041-2223-3-23","url":null,"abstract":"<p><strong>Unlabelled: </strong></p><p><strong>Background: </strong>ADH1B is one of the most studied human genes with many polymorphic sites. One of the single nucleotide polymorphism (SNP), rs1229984, coding for the Arg48His substitution, have been associated with many serious diseases including alcoholism and cancers of the digestive system. The derived allele, ADH1B*48His, reaches high frequency only in East Asia and Southwest Asia, and is highly associated with agriculture. Micro-evolutionary study has defined seven haplogroups for ADH1B based on seven SNPs encompassing the gene. Three of those haplogroups, H5, H6, and H7, contain the ADH1B*48His allele. H5 occurs in Southwest Asia and the other two are found in East Asia. H7 is derived from H6 by the derived allele of rs3811801. The H7 haplotype has been shown to have undergone significant positive selection in Han Chinese, Hmong, Koreans, Japanese, Khazak, Mongols, and so on.</p><p><strong>Methods: </strong>In the present study, we tested whether Tibetans also showed evidence for selection by typing 23 SNPs in the region covering the ADH1B gene in 1,175 individuals from 12 Tibetan populations representing all districts of the Tibet Autonomous Region. Multiple statistics were estimated to examine the gene diversities and positive selection signals among the Tibetans and other populations in East Asia.</p><p><strong>Results: </strong>The larger Tibetan populations (Qamdo, Lhasa, Nagqu, Nyingchi, Shannan, and Shigatse) comprised mostly farmers, have around 12% of H7, and 2% of H6. The smaller populations, living on hunting or recently switched to farming, have lower H7 frequencies (Tingri 9%, Gongbo 8%, Monba and Sherpa 6%). Luoba (2%) and Deng (0%) have even lower frequencies. Long-range haplotype analyses revealed very weak signals of positive selection for H7 among Tibetans. Interestingly, the haplotype diversity of H7 is higher in Tibetans than in any other populations studied, indicating a longer diversification history for that haplogroup in Tibetans. Network analysis on the long-range haplotypes revealed that H7 in the Han Chinese did not come from the Tibetans but from a common ancestor of the two populations.</p><p><strong>Conclusions: </strong>We argue that H7 of ADH1B originated in the ancestors of Sino-Tibetan populations and flowed to Tibetans very early. However, as Tibetans depend less on crops, and therefore were not significantly affected by selection. Thus, H7 has not risen to a high frequency, whereas the diversity of the haplogroup has accumulated to a very high level.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"3 1","pages":"23"},"PeriodicalIF":0.0,"publicationDate":"2012-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3528464/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31070858","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Socially responsible genetic research with descendants of the First Australians.","authors":"Sheila M van Holst Pellekaan","doi":"10.1186/2041-2223-3-22","DOIUrl":"https://doi.org/10.1186/2041-2223-3-22","url":null,"abstract":"<p><p> Aboriginal Australians, one of the world's indigenous peoples now outnumbered through colonization, are the most under-represented in genetic research because they feel that the benefits do not outweigh the social cost of involvement. Descendants of the First Australians have survived a period of European occupation during which time they were dispossessed of land, language and cultural identity resulting in inequities in health, education, and employment opportunities. Compared to Maori and Native American peoples, the ability to form organizations that help to control their affairs is very recent. The desire to control is understandably strong yet the 'gate-keeping' role of some organizations risks shifting the control away from smaller communities and has become increasingly politicized. In the past, research practices by Western scientists were poorly presented and have resulted in resistance to proposals that are perceived to have no beneficial outcomes for participants. In this age of advanced technological expertise in genetics, benefits to all humanity are clear to those carrying out research projects, yet not always to those being asked to participate, presenting extra challenges. Excellent guidelines for ethical conduct in research are available to assist researchers, prospective participants, and ethics committees or review boards that approve and monitor procedures. The essence of these guidelines are that research should be carried out with a spirit of integrity, respect, reciprocity, parity, recognition of survival and protection of social and cultural values, a need for control and shared responsibility. Specific Aboriginal organizations, with which researchers need to work to negotiate partnerships, vary within and between Australian states and will always expect Aboriginal personnel to be involved. People experienced in the consultation process are necessary as part of a team. By working patiently through lengthy negotiations with Aboriginal Australians, scientists can achieve valuable results, but failure to do so with respect and understanding will not yield hoped for outcomes. My own experience working with communities in the Darling River region of western New South Wales has been an enriching and rewarding one, with a long period of successful research lately delayed by increased expectation of monitoring and involvement at state level.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"3 1","pages":"22"},"PeriodicalIF":0.0,"publicationDate":"2012-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-3-22","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31048526","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Significant others.","authors":"Mark A Jobling","doi":"10.1186/2041-2223-3-21","DOIUrl":"https://doi.org/10.1186/2041-2223-3-21","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"3 1","pages":"21"},"PeriodicalIF":0.0,"publicationDate":"2012-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-3-21","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30987382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic view on the peopling of India.","authors":"Rakesh Tamang,&nbsp;Kumarasamy Thangaraj","doi":"10.1186/2041-2223-3-20","DOIUrl":"https://doi.org/10.1186/2041-2223-3-20","url":null,"abstract":"<p><p> India is known for its vast human diversity, consisting of more than four and a half thousand anthropologically well-defined populations. Each population differs in terms of language, culture, physical features and, most importantly, genetic architecture. The size of populations varies from a few hundred to millions. Based on the social structure, Indians are classified into various caste, tribe and religious groups. These social classifications are very rigid and have remained undisturbed by emerging urbanisation and cultural changes. The variable social customs, strict endogamy marriage practices, long-term isolation and evolutionary forces have added immensely to the diversification of the Indian populations. These factors have also led to these populations acquiring a set of Indian-specific genetic variations responsible for various diseases in India. Interestingly, most of these variations are absent outside the Indian subcontinent. Thus, this review is focused on the peopling of India, the caste system, marriage practice and the resulting health and forensic implications.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"3 1","pages":"20"},"PeriodicalIF":0.0,"publicationDate":"2012-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-3-20","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30938226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High throughput DNA sequencing to detect differences in the subgingival plaque microbiome in elderly subjects with and without dementia.","authors":"Andrew F Cockburn,&nbsp;Jonathan M Dehlin,&nbsp;Tiffany Ngan,&nbsp;Richard Crout,&nbsp;Goran Boskovic,&nbsp;James Denvir,&nbsp;Donald Primerano,&nbsp;Brenda L Plassman,&nbsp;Bei Wu,&nbsp;Christopher F Cuff","doi":"10.1186/2041-2223-3-19","DOIUrl":"https://doi.org/10.1186/2041-2223-3-19","url":null,"abstract":"<p><strong>Background: </strong>To investigate the potential association between oral health and cognitive function, a pilot study was conducted to evaluate high throughput DNA sequencing of the V3 region of the 16S ribosomal RNA gene for determining the relative abundance of bacterial taxa in subgingival plaque from older adults with or without dementia.</p><p><strong>Methods: </strong>Subgingival plaque samples were obtained from ten individuals at least 70 years old who participated in a study to assess oral health and cognitive function. DNA was isolated from the samples and a gene segment from the V3 portion of the 16S bacterial ribosomal RNA gene was amplified and sequenced using an Illumina HiSeq1000 DNA sequencer. Bacterial populations found in the subgingival plaque were identified and assessed with respect to the cognitive status and oral health of the participants who provided the samples.</p><p><strong>Results: </strong>More than two million high quality DNA sequences were obtained from each sample. Individuals differed greatly in the mix of phylotypes, but different sites from different subgingival depths in the same subject were usually similar. No consistent differences were observed in this small sample between subjects separated by levels of oral health, sex, or age; however a consistently higher level of Fusobacteriaceae and a generally lower level of Prevotellaceae was seen in subjects without dementia, although the difference did not reach statistical significance, possibly because of the small sample size.</p><p><strong>Conclusions: </strong>The results from this pilot study provide suggestive evidence that alterations in the subgingival microbiome are associated with changes in cognitive function, and provide support for an expanded analysis of the role of the oral microbiome in dementia.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"3 1","pages":"19"},"PeriodicalIF":0.0,"publicationDate":"2012-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-3-19","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30922859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}