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Dive into the research topics where Peter de Knijff is active.

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Featured researches published by Peter de Knijff.


American Journal of Human Genetics | 2000

Y-Chromosomal Diversity in Europe Is Clinal and Influenced Primarily by Geography, Rather than by Language

Zoë H. Rosser; Tatiana Zerjal; Matthew E. Hurles; Maarja Adojaan; Dragan Alavantic; António Amorim; William Amos; Manuel Armenteros; Eduardo Arroyo; Guido Barbujani; G. Beckman; L. Beckman; Jaume Bertranpetit; Elena Bosch; Daniel G. Bradley; Gaute Brede; Gillian Cooper; Helena B.S.M. Côrte-Real; Peter de Knijff; Ronny Decorte; Yuri E. Dubrova; Oleg V. Evgrafov; Anja Gilissen; Sanja Glisic; Mukaddes Gölge; Emmeline W. Hill; Anna Jeziorowska; Luba Kalaydjieva; Manfred Kayser; Toomas Kivisild

Clinal patterns of autosomal genetic diversity within Europe have been interpreted in previous studies in terms of a Neolithic demic diffusion model for the spread of agriculture; in contrast, studies using mtDNA have traced many founding lineages to the Paleolithic and have not shown strongly clinal variation. We have used 11 human Y-chromosomal biallelic polymorphisms, defining 10 haplogroups, to analyze a sample of 3,616 Y chromosomes belonging to 47 European and circum-European populations. Patterns of geographic differentiation are highly nonrandom, and, when they are assessed using spatial autocorrelation analysis, they show significant clines for five of six haplogroups analyzed. Clines for two haplogroups, representing 45% of the chromosomes, are continentwide and consistent with the demic diffusion hypothesis. Clines for three other haplogroups each have different foci and are more regionally restricted and are likely to reflect distinct population movements, including one from north of the Black Sea. Principal-components analysis suggests that populations are related primarily on the basis of geography, rather than on the basis of linguistic affinity. This is confirmed in Mantel tests, which show a strong and highly significant partial correlation between genetics and geography but a low, nonsignificant partial correlation between genetics and language. Genetic-barrier analysis also indicates the primacy of geography in the shaping of patterns of variation. These patterns retain a strong signal of expansion from the Near East but also suggest that the demographic history of Europe has been complex and influenced by other major population movements, as well as by linguistic and geographic heterogeneities and the effects of drift.


Genetics | 2005

The Role of Selection in the Evolution of Human Mitochondrial Genomes

Toomas Kivisild; Peidong Shen; Dennis P. Wall; Bao H. Do; Raphael Sung; Karen Davis; Giuseppe Passarino; Peter A. Underhill; Curt Scharfe; Antonio Torroni; Rosaria Scozzari; David Modiano; Alfredo Coppa; Peter de Knijff; Marcus W. Feldman; Luca Cavalli-Sforza; Peter J. Oefner

High mutation rate in mammalian mitochondrial DNA generates a highly divergent pool of alleles even within species that have dispersed and expanded in size recently. Phylogenetic analysis of 277 human mitochondrial genomes revealed a significant (P < 0.01) excess of rRNA and nonsynonymous base substitutions among hotspots of recurrent mutation. Most hotspots involved transitions from guanine to adenine that, with thymine-to-cytosine transitions, illustrate the asymmetric bias in codon usage at synonymous sites on the heavy-strand DNA. The mitochondrion-encoded tRNAThr varied significantly more than any other tRNA gene. Threonine and valine codons were involved in 259 of the 414 amino acid replacements observed. The ratio of nonsynonymous changes from and to threonine and valine differed significantly (P = 0.003) between populations with neutral (22/58) and populations with significantly negative Tajimas D values (70/76), independent of their geographic location. In contrast to a recent suggestion that the excess of nonsilent mutations is characteristic of Arctic populations, implying their role in cold adaptation, we demonstrate that the surplus of nonsynonymous mutations is a general feature of the young branches of the phylogenetic tree, affecting also those that are found only in Africa. We introduce a new calibration method of the mutation rate of synonymous transitions to estimate the coalescent times of mtDNA haplogroups.


Science | 2011

An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia

Morten Rasmussen; Xiaosen Guo; Yong Wang; Kirk E. Lohmueller; Simon Rasmussen; Anders Albrechtsen; Line Skotte; Stinus Lindgreen; Mait Metspalu; Thibaut Jombart; Toomas Kivisild; Weiwei Zhai; Anders Eriksson; Andrea Manica; Ludovic Orlando; Francisco M. De La Vega; Silvana R. Tridico; Ene Metspalu; Kasper Nielsen; María C. Ávila-Arcos; J. Víctor Moreno-Mayar; Craig Muller; Joe Dortch; M. Thomas P. Gilbert; Ole Lund; Agata Wesolowska; Monika Karmin; Lucy A. Weinert; Bo Wang; Jun Li

Whole-genome data indicate that early modern humans expanded into Australia 62,000 to 75,000 years ago. We present an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. We detect no evidence of European admixture and estimate contamination levels to be below 0.5%. We show that Aboriginal Australians are descendants of an early human dispersal into eastern Asia, possibly 62,000 to 75,000 years ago. This dispersal is separate from the one that gave rise to modern Asians 25,000 to 38,000 years ago. We also find evidence of gene flow between populations of the two dispersal waves prior to the divergence of Native Americans from modern Asian ancestors. Our findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia, likely representing one of the oldest continuous populations outside Africa.


American Journal of Human Genetics | 2000

Characteristics and frequency of germline mutations at microsatellite loci from the human Y chromosome, as revealed by direct observation in father/son pairs.

Manfred Kayser; Lutz Roewer; Minttu Hedman; Lotte Henke; Jürgen Henke; Silke Brauer; Carmen Krüger; Michael Krawczak; Marion Nagy; Tadeusz Dobosz; Reinhard Szibor; Peter de Knijff; Mark Stoneking; Antti Sajantila

A number of applications of analysis of human Y-chromosome microsatellite loci to human evolution and forensic science require reliable estimates of the mutation rate and knowledge of the mutational mechanism. We therefore screened a total of 4,999 meioses from father/son pairs with confirmed paternity (probability >/=99. 9%) at 15 Y-chromosomal microsatellite loci and identified 14 mutations. The locus-specific mutation-rate estimates were 0-8. 58x10-3, and the average mutation rate estimates were 3.17x10-3 (95% confidence interval [CI] 1.89-4.94x10-3) across 8 tetranucleotide microsatellites and 2.80x10-3 (95% CI 1.72-4.27x10-3) across all 15 Y-chromosomal microsatellites studied. Our data show a mutational bias toward length increase, on the basis of observation of more repeat gains than losses (10:4). The data are in almost complete agreement with the stepwise-mutation model, with 13 single-repeat changes and 1 double-repeat change. Sequence analysis revealed that all mutations occurred in uninterrupted homogenous arrays of >/=11 repeats. We conclude that mutation rates and characteristics of human Y-chromosomal microsatellites are consistent with those of autosomal microsatellites. This indicates that the general mutational mechanism of microsatellites is independent of recombination.


Nature Genetics | 2014

Whole-genome sequence variation, population structure and demographic history of the Dutch population

Laurent C. Francioli; Androniki Menelaou; Sara L. Pulit; Freerk van Dijk; Pier Francesco Palamara; Clara C. Elbers; Pieter B. T. Neerincx; Kai Ye; Victor Guryev; Wigard P. Kloosterman; Patrick Deelen; Abdel Abdellaoui; Elisabeth M. van Leeuwen; Mannis van Oven; Martijn Vermaat; Mingkun Li; Jeroen F. J. Laros; Lennart C. Karssen; Alexandros Kanterakis; Najaf Amin; Jouke-Jan Hottenga; Eric-Wubbo Lameijer; Mathijs Kattenberg; Martijn Dijkstra; Heorhiy Byelas; Jessica van Setten; Barbera D. C. van Schaik; Jan Bot; Isaac J. Nijman; Ivo Renkens

Whole-genome sequencing enables complete characterization of genetic variation, but geographic clustering of rare alleles demands many diverse populations be studied. Here we describe the Genome of the Netherlands (GoNL) Project, in which we sequenced the whole genomes of 250 Dutch parent-offspring families and constructed a haplotype map of 20.4 million single-nucleotide variants and 1.2 million insertions and deletions. The intermediate coverage (∼13×) and trio design enabled extensive characterization of structural variation, including midsize events (30–500 bp) previously poorly catalogued and de novo mutations. We demonstrate that the quality of the haplotypes boosts imputation accuracy in independent samples, especially for lower frequency alleles. Population genetic analyses demonstrate fine-scale structure across the country and support multiple ancient migrations, consistent with historical changes in sea level and flooding. The GoNL Project illustrates how single-population whole-genome sequencing can provide detailed characterization of genetic variation and may guide the design of future population studies.


The New England Journal of Medicine | 1998

Polymorphisms in the Coagulation Factor VII Gene and the Risk of Myocardial Infarction

Licia Iacoviello; Augusto Di Castelnuovo; Peter de Knijff; A. D'Orazio; C. Amore; Rosa Arboretti; Cornelis Kluft; Maria Benedetta Donati

BACKGROUND High blood levels of coagulation factor VII are associated with a risk of ischemic vascular disease. Although factor VII levels may be genetically determined, the relation between genetic polymorphisms of factor VII, factor VII blood levels, and the risk of myocardial infarction has not been established. METHODS We performed a case-control study of 165 patients with familial myocardial infarction (mean [+/-SD] age, 55+/-9 years) and 225 controls without a personal or family history of cardiovascular disease (mean age, 56+/-8 years). The polymorphisms involving R353Q and hypervariable region 4 of the factor VII gene were studied. Factor VII clotting activity and antigen levels were also measured. RESULTS Patients with the QQ or H7H7 genotype had a decreased risk of myocardial infarction (odds ratios, 0.08 [95 percent confidence interval, 0.01 to 0.9] and 0.22 [95 percent confidence interval, 0.08 to 0.63], respectively). For the R353Q polymorphism, the RR genotype was associated with the highest risk, followed by the RQ genotype and then by the QQ genotype (P<0.001). For the polymorphism involving hypervariable region 4, the combined H7H5 and H6H5 genotypes were associated with the highest risk, followed in descending order by the H6H6, H6H7, and H7H7 genotypes (P<0.001). Patients with the QQ or H7H7 genotype had lower levels of both factor VII antigen and factor VII clotting activity than those with the RR or H6H6 genotype. Patients with the lowest level of factor VII clotting activity had a lower risk of myocardial infarction than those with the highest level (odds ratio, 0.13; 95 percent confidence interval, 0.05 to 0.34). CONCLUSIONS Our findings suggest that certain polymorphisms of the factor VII gene may influence the risk of myocardial infarction. It is possible that this effect may be mediated by alterations in factor VII levels.


Nature Reviews Genetics | 2011

Improving human forensics through advances in genetics, genomics and molecular biology

Manfred Kayser; Peter de Knijff

Forensic DNA profiling currently allows the identification of persons already known to investigating authorities. Recent advances have produced new types of genetic markers with the potential to overcome some important limitations of current DNA profiling methods. Moreover, other developments are enabling completely new kinds of forensically relevant information to be extracted from biological samples. These include new molecular approaches for finding individuals previously unknown to investigators, and new molecular methods to support links between forensic sample donors and criminal acts. Such advances in genetics, genomics and molecular biology are likely to improve human forensic case work in the near future.


American Journal of Human Genetics | 2010

Mutability of Y-chromosomal microsatellites: rates, characteristics, molecular bases, and forensic implications.

Kaye N. Ballantyne; Miriam Goedbloed; Rixun Fang; Onno Schaap; Oscar Lao; Andreas Wollstein; Ying Choi; Kate van Duijn; Mark Vermeulen; Silke Brauer; Ronny Decorte; Micaela Poetsch; Nicole von Wurmb-Schwark; Peter de Knijff; Damian Labuda; Hélène Vézina; Hans Knoblauch; Rüdiger Lessig; Lutz Roewer; Rafał Płoski; Tadeusz Dobosz; Lotte Henke; Jürgen Henke; Manohar R. Furtado; Manfred Kayser

Nonrecombining Y-chromosomal microsatellites (Y-STRs) are widely used to infer population histories, discover genealogical relationships, and identify males for criminal justice purposes. Although a key requirement for their application is reliable mutability knowledge, empirical data are only available for a small number of Y-STRs thus far. To rectify this, we analyzed a large number of 186 Y-STR markers in nearly 2000 DNA-confirmed father-son pairs, covering an overall number of 352,999 meiotic transfers. Following confirmation by DNA sequence analysis, the retrieved mutation data were modeled via a Bayesian approach, resulting in mutation rates from 3.78 × 10(-4) (95% credible interval [CI], 1.38 × 10(-5) - 2.02 × 10(-3)) to 7.44 × 10(-2) (95% CI, 6.51 × 10(-2) - 9.09 × 10(-2)) per marker per generation. With the 924 mutations at 120 Y-STR markers, a nonsignificant excess of repeat losses versus gains (1.16:1), as well as a strong and significant excess of single-repeat versus multirepeat changes (25.23:1), was observed. Although the total repeat number influenced Y-STR locus mutability most strongly, repeat complexity, the length in base pairs of the repeated motif, and the fathers age also contributed to Y-STR mutability. To exemplify how to practically utilize this knowledge, we analyzed the 13 most mutable Y-STRs in an independent sample set and empirically proved their suitability for distinguishing close and distantly related males. This finding is expected to revolutionize Y-chromosomal applications in forensic biology, from previous male lineage differentiation toward future male individual identification.


American Journal of Human Genetics | 2001

An Extensive Analysis of Y-Chromosomal Microsatellite Haplotypes in Globally Dispersed Human Populations

Manfred Kayser; Michael Krawczak; Laurent Excoffier; Patrick Dieltjes; Daniel Corach; Vincente Pascali; Christian Gehrig; Luigi F. Bernini; Jørgen Jespersen; Egbert Bakker; Lutz Roewer; Peter de Knijff

The genetic variance at seven Y-chromosomal microsatellite loci (or short tandem repeats [STRs]) was studied among 986 male individuals from 20 globally dispersed human populations. A total of 598 different haplotypes were observed, of which 437 (73.1%) were each found in a single male only. Population-specific haplotype-diversity values were.86-.99. Analyses of haplotype diversity and population-specific haplotypes revealed marked population-structure differences between more-isolated indigenous populations (e.g., Central African Pygmies or Greenland Inuit) and more-admixed populations (e.g., Europeans or Surinamese). Furthermore, male individuals from isolated indigenous populations shared haplotypes mainly with male individuals from their own population. By analysis of molecular variance, we found that 76.8% of the total genetic variance present among these male individuals could be attributed to genetic differences between male individuals who were members of the same population. Haplotype sharing between populations, phi(ST) statistics, and phylogenetic analysis identified close genetic affinities among European populations and among New Guinean populations. Our data illustrate that Y-chromosomal STR haplotypes are an ideal tool for the study of the genetic affinities between groups of male subjects and for detection of population structure.


Lancet Oncology | 2010

SDHAF2 mutations in familial and sporadic paraganglioma and phaeochromocytoma

Jean-Pierre Bayley; H.P.M. Kunst; Alberto Cascón; M. L. Sampietro; José Gaal; Esther Korpershoek; Adolfo Hinojar-Gutierrez; Henri Timmers; Lies H. Hoefsloot; Mario Hermsen; Carlos Suárez; A. Karim Hussain; Annette H. J. T. Vriends; Frederik J. Hes; Jeroen C. Jansen; Carli M. J. Tops; Eleonora P. M. Corssmit; Peter de Knijff; Jacques W. M. Lenders; C.W.R.J. Cremers; Peter Devilee; Winand N. M. Dinjens; Ronald R. de Krijger; Mercedes Robledo

BACKGROUND Paragangliomas and phaeochromocytomas are neuroendocrine tumours associated frequently with germline mutations of SDHD, SDHC, and SDHB. Previous studies have shown the imprinted SDHAF2 gene to be mutated in a large Dutch kindred with paragangliomas. We aimed to identify SDHAF2 mutation carriers, assess the clinical genetic significance of SDHAF2, and describe the associated clinical phenotype. METHODS We undertook a multicentre study in Spain and The Netherlands in 443 apparently sporadic patients with paragangliomas and phaeochromocytomas who did not have mutations in SDHD, SDHC, or SDHB. We analysed DNA of 315 patients for germline mutations of SDHAF2; a subset (n=200) was investigated for gross gene deletions. DNA from a group of 128 tumours was studied for somatic mutations. We also examined a Spanish family with head and neck paragangliomas with a young age of onset for the presence of SDHAF2 mutations, undertook haplotype analysis in this kindred, and assessed their clinical phenotype. FINDINGS We did not identify any germline or somatic mutations of SDHAF2, and no gross gene deletions were noted in the subset of apparently sporadic patients analysed. Investigation of the Spanish family identified a pathogenic germline DNA mutation of SDHAF2, 232G-->A (Gly78Arg), identical to the Dutch kindred. INTERPRETATION SDHAF2 mutations do not have an important role in phaeochromocytoma and are rare in head and neck paraganglioma. Identification of a second family with the Gly78Arg mutation suggests that this is a crucial residue for the function of SDHAF2. We conclude that SDHAF2 mutation analysis is justified in very young patients with isolated head and neck paraganglioma without mutations in SDHD, SDHC, or SDHB, and in individuals with familial antecedents who are negative for mutations in all other risk genes. FUNDING Dutch Cancer Society, European Union 6th Framework Program, Fondo Investigaciones Sanitarias, Fundación Mutua Madrileña, and Red Temática de Investigación Cooperativa en Cáncer.

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Kristiaan J. van der Gaag

Leiden University Medical Center

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Manfred Kayser

Erasmus University Rotterdam

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Chris Tyler-Smith

Wellcome Trust Sanger Institute

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Thirsa Kraaijenbrink

Leiden University Medical Center

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Titia Sijen

Netherlands Forensic Institute

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Sofia Zuniga

Leiden University Medical Center

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Jeroen F. J. Laros

Leiden University Medical Center

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