| 1. |
- Forrest, ARR, et al.
(författare)
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A promoter-level mammalian expression atlas
- 2014
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 507:7493, s. 462-
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Noguchi, S, et al.
(författare)
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FANTOM5 CAGE profiles of human and mouse samples
- 2017
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Ingår i: Scientific data. - : Springer Science and Business Media LLC. - 2052-4463. ; 4, s. 170112-
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Tidskriftsartikel (refereegranskat)abstract
- In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.
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| 3. |
- Sikora, M., et al.
(författare)
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The population history of northeastern Siberia since the Pleistocene
- 2019
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 570:7760
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Tidskriftsartikel (refereegranskat)abstract
- Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of 'Ancient North Siberians' who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to 'Ancient Palaeo-Siberians' who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name 'Neo-Siberians', and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.
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| 4. |
- Lao, O., et al.
(författare)
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Correlation between Genetic and Geographic Structure in Europe
- 2008
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Ingår i: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 18:16, s. 1241-1248
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the genetic structure of the European population is important, not only from a historical perspective, but also for the appropriate design and interpretation of genetic epidemiological studies. Previous population genetic analyses with autosomal markers in Europe either had a wide geographic but narrow genomic coverage [1, 2], or vice versa [3-6]. We therefore investigated Affymetrix GeneChip 500K genotype data from 2,514 individuals belonging to 23 different subpopulations, widely spread over Europe. Although we found only a low level of genetic differentiation between subpopulations, the existing differences were characterized by a strong continent-wide correlation between geographic and genetic distance. Furthermore, mean heterozygosity was larger, and mean linkage disequilibrium smaller, in southern as compared to northern Europe. Both parameters clearly showed a clinal distribution that provided evidence for a spatial continuity of genetic diversity in Europe. Our comprehensive genetic data are thus compatible with expectations based upon European population history, including the hypotheses of a south-north expansion and/or a larger effective population size in southern than in northern Europe. By including the widely used CEPH from Utah (CEU) samples into our analysis, we could show that these individuals represent northern and western Europeans reasonably well, thereby confirming their assumed regional ancestry. © 2008 Elsevier Ltd. All rights reserved.
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| 5. |
- Ballantyne, Kaye N., et al.
(författare)
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Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats
- 2014
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Ingår i: Human Mutation. - : John Wiley & Sons. - 1059-7794 .- 1098-1004. ; 35:8, s. 1021-1032
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Tidskriftsartikel (refereegranskat)abstract
- Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, greater than99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836-0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 father-son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RMY-STRs in identifying and separating unrelated and related males and provides a reference database.
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| 6. |
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| 7. |
- Lazaridis, Iosif, et al.
(författare)
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Ancient human genomes suggest three ancestral populations for present-day Europeans
- 2014
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 513:7518, s. 409-
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Tidskriftsartikel (refereegranskat)abstract
- We sequenced the genomes of a similar to 7,000-year-old farmer from Germany and eight similar to 8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes(1-4) with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians(3), who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations' deep relationships and show that early European farmers had similar to 44% ancestry from a 'basal Eurasian' population that split before the diversification of other non-African lineages.
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| 8. |
- Lahti, R. A., et al.
(författare)
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Cause and manner of death and phase of the blood alcohol curve
- 2014
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Ingår i: Forensic Science International. - : Elsevier. - 0379-0738 .- 1872-6283. ; 244, s. 306-312
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Tidskriftsartikel (refereegranskat)abstract
- In a large number of forensic autopsies (N = 28,184) the concentrations of ethanol in femoral blood and bladder urine were determined and the urine-to-blood concentration ratios of ethanol were calculated. Based on the differences in ethanol concentration between urine and blood, the deaths were classified as having occurred during the absorptive, the peak or the post-absorptive phase of the blood-alcohol curve. Most people died in the post-absorptive phase, N = 24,223 (86%), whereas 1538 individuals (5.5%) were still absorbing alcohol and 2423 (8.6%) were at or close to the peak BAC at time of death. Both blood-alcohol concentration (BAC) and urine-alcohol concentration (UAC) were significantly higher in the post-absorptive phase (p less than 0.001). The proportions of people dying in the absorptive and peak phases increased with advancing age. The cause of death (CoD) and manner of death (MoD) according to death certificates were compared with phase of the blood-alcohol curve using amultinomial regression model with and without making adjustment for possible effects of age, gender and BAC. The relative risk (RR) and relative risk ratios (RRR) showed some associations between CoD and phase of the blood-alcohol curve. Undetermined MoD was significantly higher in the absorptive phase compared with the post-absorptive phase (RRR = 2.12). Deaths related to esophagus, stomach and duodenum (RRR = 2.04) and alcoholic liver diseases (RRR = 1.85) were significantly higher at or close to peak phase compared to the post-absorptive phase. Road-traffic fatalities were more prevalent in the peak BAC phase (RRR = 1.33) and deaths by accidental falls were less in the absorptive phase (RRR = 0.58) compared with the post-absorptive phase. The phase of alcohol intoxication seems relevant to consider by forensic experts when alcohol-related deaths are investigated.
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| 9. |
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| 10. |
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| 11. |
- Vuorio, A F, et al.
(författare)
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Amplification of the hypervariable region close to the apolipoprotein B gene : application to forensic problems
- 1990
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Ingår i: Biochemical and Biophysical Research Communications - BBRC. - 0006-291X .- 1090-2104. ; 170:2, s. 616-620
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Tidskriftsartikel (refereegranskat)abstract
- Our purpose was to identify individuals from blood stains in two murder cases. We used primers flanking the hypervariable region of the apoB gene to amplify DNA extracted from blood stains and blood samples from suspected persons. The sensitivity and specificity of the procedure was improved by carrying out two consecutive PCR amplifications with a nested set of primers in the second amplification. The size of the generated fragments was determined by polyacrylamide gel electrophoresis followed by staining with ethidium bromide. By comparing the fragments produced from the stains with those from the blood samples we were able to identify the origin of the blood stains in both cases.
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| 12. |
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| 13. |
- Pacek, P, et al.
(författare)
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Determination of allele frequencies at loci with length polymorphism by quantitative analysis of DNA amplified from pooled samples
- 1993
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Ingår i: PCR methods and applications. - : Cold Spring Harbor Laboratory. - 1054-9803. ; 2:4, s. 313-317
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Tidskriftsartikel (refereegranskat)abstract
- We present a new method that allows rapid determination of allele frequencies at loci exhibiting length polymorphism. In this method a fluorescence-labeled PCR primer is used to amplify the polymorphic region from pooled DNA samples originating from a large number of individuals. The fluorescent PCR products are separated by gel electrophoresis on an automatic DNA sequencer and the relative amount of the PCR products are determined. The distribution of the PCR products obtained from the alleles present in the pooled samples directly corresponds to the allele frequency in the population in question. The allele frequencies at a short tandem repeat locus in the von Willebrand factor gene and at the D1S80 locus were determined in the Finnish population. We found that the allele frequencies determined by quantitative analysis of PCR products from pooled DNA samples and by analyzing individual samples were in good agreement.
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| 14. |
- Sajantila, A, et al.
(författare)
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A microsatellite polymorphism in the von Willebrand factor gene : comparison of allele frequencies in different population samples and evaluation for forensic medicine
- 1994
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Ingår i: Forensic Science International. - 0379-0738 .- 1872-6283. ; 68:2, s. 91-102
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Tidskriftsartikel (refereegranskat)abstract
- The allele frequencies at the tetranucleotide repeat (TCTA) vWA locus in the vWF gene were determined in the general Finnish population, in a population representing an internal isolate of Finland, in the Vologda-Russian population, and in US Black population samples. The allele and genotype frequencies from these population samples were compared with each other and with those reported from Spanish and British population samples. Statistically significant differences were demonstrated between most of the different groups (Finns vs. Vologda-Russians, Finns vs. US Blacks, Finns vs. Spanish, Vologda-Russians vs. US Blacks, Vologda-Russians vs. Spanish, US Blacks vs. Spanish and US Blacks vs. British Caucasians), but not between the two Caucasoid population samples from Finland and Great Britain, nor between or within the subpopulation samples from Finland and those from Vologda-Russia. In addition, the vWA marker was evaluated and demonstrated to be reliable for forensic purposes and paternity testing.
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| 15. |
- Sajantila, A, et al.
(författare)
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Paternal and maternal DNA lineages reveal a bottleneck in the founding of the Finnish population
- 1996
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 93:21, s. 12035-12039
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Tidskriftsartikel (refereegranskat)abstract
- An analysis of Y-chromosomal haplotypes in several European populations reveals an almost monomorphic pattern in the Finns, whereas Y-chromosomal diversity is significantly higher in other populations. Furthermore, analyses of nucleotide positions in the mitochondrial control region that evolve slowly show a decrease in genetic diversity in Finns. Thus, relatively few men and women have contributed the genetic lineages that today survive in the Finnish population. This is likely to have caused the so-called ''Finnish disease heritage''-i.e., the occurrence of several genetic diseases in the Finnish population that are rare elsewhere. A preliminary analysis of the mitochondrial mutations that have accumulated subsequent to the bottleneck suggests that it occurred about 4000 years ago, presumably when populations using agriculture and animal husbandry arrived in Finland.
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| 16. |
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| 17. |
- Syvänen, Ann-Christine, et al.
(författare)
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Forensic DNA typing by the solid-phase minisequencing method
- 1993
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Ingår i: EXS. - 1023-294X. ; 67, s. 275-282
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Tidskriftsartikel (refereegranskat)abstract
- We describe a method for DNA-typing, in which a panel of biallelic markers are detected by the solid-phase minisequencing method (Syvänen et al., 1990). This method identifies single nucleotide variations in DNA fragments amplified by the PCR. Determination of the panel of 12 markers selected in this study proved to be an efficient and reliable method for forensic identification of individuals. We also introduce a novel approach for rapid determination of allele frequencies by quantitative analysis of pooled DNA samples.
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| 18. |
- Syvänen, Ann-Christine, et al.
(författare)
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Identification of individuals by analysis of biallelic DNA markers, using PCR and solid-phase minisequencing
- 1993
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Ingår i: American Journal of Human Genetics. - 0002-9297 .- 1537-6605. ; 52:1, s. 46-59
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Tidskriftsartikel (refereegranskat)abstract
- We have developed a new method for forensic identification of individuals, in which a panel of biallelic DNA markers are amplified by the PCR, and the variable nucleotides are detected in the amplified DNA fragments by the solid-phase minisequencing method. A panel of 12 common polymorphic nucleotides located on different chromosomes with reported allele frequencies close to .5 were chosen for the test. The allele frequencies for most of the markers were found to be similar in the Finnish and other Caucasian populations. We also introduce a novel approach for rapid determination of the population frequencies of biallelic markers. By this approach we were able to determine the allele frequencies of the markers in the Finnish population, by quantitative analysis of three pooled DNA samples representing 3,000 individuals. The power of discrimination and exclusion of the solid-phase minisequencing typing test with 12 markers was similar to that of three VNTR markers that are routinely used in forensic analyses at our institute. The solid-phase minisequencing method was successfully applied to type paternity and forensic case samples. We also show that the quantitative nature of our method allows typing of mixed samples.
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