Walther Parson

Evaluation of Y-chromosomal STRs: a multicenter study

Abstract A multicenter study has been carried out to characterize 13 polymorphic short tandem repeat (STR) systems located on the male specific part of the human Y chromosome (DYS19, DYS288, DYS385, DYS388, DYS389I/II, DYS390, DYS391, DYS392, DYS393, YCAI, YCAII, YCAIII, DXYS156Y). Amplification parameters and electrophoresis protocols including multiplex approaches were compiled. The typing of non-recombining Y loci with uniparental inheritance requires special attention to population substructuring due to prevalent male lineages. To assess the extent of these subheterogeneities up to 3825 unrelated males were typed in up to 48 population samples for the respective loci. A consistent repeat based nomenclature for most of the loci has been introduced. Moreover we have estimated the average mutation rate for DYS19 in 626 confirmed father-son pairs as 3.2 × 10–3 (95% confidence interval limits of 0.00041–0.00677), a value which can also be expected for other Y-STR loci with similar repeat structure. Recommendations are given for the forensic application of a basic set of 7 STRs (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393) for standard Y-haplotyping in forensic and paternity casework. We recommend further the inclusion of the highly polymorphic bilocal Y-STRs DYS385, YCAII, YCAIII for a nearly complete individualisation of almost any given unrelated male individual. Together, these results suggest that Y-STR loci are useful markers to identify males and male lineages in forensic practice.

Lack of Antibody Production Following Immunization in Old Age: Association with CD8+CD28− T Cell Clonal Expansions and an Imbalance in the Production of Th1 and Th2 Cytokines

Although it is generally recognized that the function of the immune system declines with age, the nature of the underlying defects is still poorly understood. We now demonstrate the predominance of CD8+CD28− T cell clonal expansions in elderly persons who fail to produce specific Abs following influenza vaccination. These clones express effector cell markers and are mostly CD45RA+. When isolated and put into culture, they are unable to proliferate, but produce IFN-γ (but no IL-5) upon stimulation with anti-CD3 or autoantigen. These autoreactive CD8+ type 1 effector cells seem to trigger a Th1 polarization, as CD4+ T cells from elderly persons without in vivo Ab production produce Th1, but only low amounts of Th2 cytokines upon in vitro stimulation with PHA. Therefore, the increased occurrence of CD8+CD28− clonal expansions may be decisive for the development of immune deficiency in the elderly.

Correlation between Genetic and Geographic Structure in Europe

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.

Chromosome Y microsatellites : population genetic and evolutionary aspects

Abstract By means of a multicenter study, a large number of males have been characterized for Y-chromosome specific short tandem repeats (STRs) or microsatellites. A complete summary of the allele frequency distributions for these Y-STRs is presented in the Appendix. This manuscript describes in more detail some of the population genetic and evolutionary aspects for a restricted set of seven chromosome Y STRs in a selected number of population samples. For all the chromosome Y STRs markedly different region-specific allele frequency distributions were observed, also when closely related populations were compared. Haplotype analyses using AMOVA showed that when four different European male groups (Germans, Dutch, Swiss, Italians) were compared, less than 10% of the total genetic variability was due to differences between these populations. Nevertheless, these pairwise comparisons revealed significant differences between most population pairs. Assuming a step-wise mutation model and a mutation frequency of 0.21%, it was estimated that chromosome Y STR-based evolutionary lines of descent can be reliably inferred over a time-span of only 1950 generations (or about 49000 years). This reduces the reliability of the inference of population affinities to a historical, rather than evolutionary time scale. This is best illustrated by the construction of a human evolutionary tree based on chromosome Y STRs in which most of the branches connect in a markedly different way compared with trees based on classical protein polymorphisms and/or mtDNA sequence variation. Thus, the chromosome Y STRs seem to be very useful in comparing closely related populations which cannot probably be separated by e.g. autosomal STRs. However, in order to be used in an evolutionary context they need to be combined with more stable Y-polymorphisms e.g. base-substitutions.

Publication of population data for forensic purposes

In 2000 a new policy concerning the publication of population genetic data was set up in Forensic Science International [1] with the introduction of a new section entitled ‘‘Announcement of population data’’. The idea was to facilitate the publication of this type of data since the use of reliable allele or haplotype frequency estimates of the polymorphisms is a requirement in most countries, both in forensic and in paternity cases. Announcements of population data consisted in short communications under a fixed format, avoiding the repetition of superfluous information (i.e., materials and methods) and concentrating the message on the key information needed for the use of genetic data for forensic and population genetics. In our opinion, this type of paper completely fulfilled the aims of the editors and, even more importantly, has made an essential contribution to the dissemination of common standards all over the world. In addition they have motivated forensic practitioners (especially in countries with little development in forensic genetics) to introduce themselves in forensic research. With the launch of the new journal, we decided to continue the same policy as a first step but keeping in mind that we have to move forward to increase the quality of the journal and to avoid having a journal exclusively devoted to announcements of population genetic data. The number of population genetic papers from the very beginning has continuously increased, representing now more than 60% of the submissions to the journal. Therefore, it is time to raise the threshold regarding the acceptance of this type of publication but taking into account the importance of the dissemination of standards and the motivation that this type of research represents for some groups and countries. For this reason, we have decided to move to a next step and to introduce a new section on Forensic Population Genetics in the journal. Manuscripts with population genetic content can be submitted to this section at http://www.ees.elsevier.com/fsigen/ using three types of formats: Forensic Population Genetics – Original papers: in this section full length papers on relevant population genetics issues of forensic interest will be considered for publication. The data should be original, the population genetic analysis must be of the highest quality and the data should have forensic relevance beyond the scope of simply reporting allele or haplotype frequencies. Forensic Population Genetics – Short communications: understanding that both the quality of population data and the relevance of results are crucial, short communications will have the format of the former ‘‘Announcements of population data’’ with some changes (see below) in order to guarantee their quality.

EMPOP—A forensic mtDNA database

Mitochondrial DNA databases stand as the basis for frequency estimations of mtDNA sequences that became relevant in a case. The establishment of mtDNA databases sounds trivial; however, it has been shown in the past that this undertaking is prone to error for several reasons, particularly human error. We have established a concept for mtDNA data generation, analysis, transfer and quality control that meets forensic standards. Due to the complexity of mtDNA population data tables it is often difficult if not impossible to detect errors, especially for the untrained eye. We developed software based on quasi-median network analysis that visualizes mtDNA data tables and thus signposts sequencing, interpretation and transcription errors. The mtDNA data (N=5173; release 1) are stored and made publicly available via the Internet in the form of the EDNAP mtDNA Population Database, short EMPOP. This website also facilitates quasi-median network analysis and provides results that can be used to check the quality of mtDNA sequence data. EMPOP has been launched on 16 October 2006 and is since then available at http://www.empop.org.

New guidelines for the publication of genetic population data.

In 2000 a new policy concerning the publication of population genetic data was set up in Forensic Science International [1] with the introduction of a new section entitled ‘‘Announcement of population data’’. Subsequently in 2010 [2] a new section on ‘‘Forensic Population Genetics’’ was introduced, and recommendations were redefined. FSI: Genetics is one of the few journals still considering population genetic data for publication and we strongly believe that this policy has contributed to the dissemination of common standards in the field all over the world and also to motivate labs and people to embark in research in the area of forensic genetics. For this reason it is our intention to continue with this policy, and recently an associate editor exclusively devoted to this topic was appointed to the journal. Despite having defined a more detailed procedure for acceptance, our journal is still receiving a massive number of submissions of varying quality in this area. Therefore it has become necessary to raise the threshold regarding the acceptance of this type of publication to ensure a high standard of published data. In addition we want to improve the submission, reviewing and publication procedures, and to correct some aspects that we have detected such as the obligation to meet ethical standards in the collection of samples including informed consent and approval by ethical committees. For this reason, we have decided to publish new guidelines for the publication of population genetic data in the journal.

Consistent treatment of length variants in the human mtDNA control region: a reappraisal

In forensic science, as well as in molecular anthropology and medical genetics, human mitochondrial DNA (mtDNA) variation is being recorded by aligning mtDNA sequences to the revised Cambridge reference sequence (rCRS). This task is straightforward for the vast majority of nucleotide positions but appears to be difficult for some short sequence stretches, namely, in regions displaying length variation. Earlier guidelines for imposing a unique alignment relied on binary alignment to a standard sequence (the rCRS) and used additional priority rules for resolving ambiguities. It turns out, however, that these rules have not been applied rigorously and led to inconsistent nomenclature. There is no way to adapt the priority rules in a reasonable way because binary alignment to a standard sequence is bound to produce artificial alignments that may place sequences separated by a single mutation at mismatch distance larger than 1. To remedy the situation, we propose a phylogenetic approach for multiple alignment and resulting notation.

Update of the guidelines for the publication of genetic population data

Due to the massive number of submissions of varying quality with population genetic data we decided one year ago to raise the threshold regarding the acceptance of this type of publications to ensure a high standard of published data and, therefore, we updated the FSI: Genetics 2010 guidelines [1] to a new set of recommendations [2]. In the 2013 guidelines in addition to some new requirements in the procedure and regarding ethical standards, we significantly increased the number of markers and samples required for submission to the journal of papers presenting population data alone, with no additional information on new methods or other forensically relevant findings. We have been working during last year with these new recommendations. During this period, we have received a number of critical comments from authors that we have considered and therefore we have decided to make some amendments in the requirements. The first change refers to the minimal number of autosomal STRs. The 2013 guidelines indicate that for data comprising autosomal STR genotypes only, 17 different autosomal STR loci are required as a minimum. This was based on the average number of STRs that most laboratories are routinely using – in most cases forensic laboratories are using at least two PCR multiplexes (commercial kits or homemade) on their routine work for a minimal number of 17 autosomal STR markers. However, this number would exclude laboratories and national and international compilation efforts that are working with just one kit, for some of the most commonly used kits. Whilst we certainly recognize the need to restrict the number of small data sets submitted we think that the forensic community would benefit from the publication of a large and nationally important data set such as the ones that are being generated in some countries. For this reason we have decided to reinstate the 2010 recommendations requiring 15 STRs only. Concerning X chromosome a minimum number of 12 STRs will be required and for the Y chromosome a minimum of 17 STRs will be required as well, taking into account that the core minimum haplotype (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385) [3,4] must be provided if it has not been previously analyzed in the same population sample. Collaborative efforts to produce large datasets are strongly encouraged and, therefore, the minimal number of markers should not be a limitation to the publication of large National or International collaborative databasing efforts when a significant number of laboratories and samples are involved. There are also changes in the requirements for the minimum number of samples. We maintain the threshold of 500 samples for

Inhibition of the acetyltransferases p300 and CBP reveals a targetable function for p300 in the survival and invasion pathways of prostate cancer cell lines

Inhibitors of histone deacetylases have been approved for clinical application in cancer treatment. On the other hand, histone acetyltransferase (HAT) inhibitors have been less extensively investigated for their potential use in cancer therapy. In prostate cancer, the HATs and coactivators p300 and CBP are upregulated and may induce transcription of androgen receptor (AR)-responsive genes, even in the absence or presence of low levels of AR. To discover a potential anticancer effect of p300/CBP inhibition, we used two different approaches: (i) downregulation of p300 and CBP by specific short interfering RNA (siRNA) and (ii) chemical inhibition of the acetyltransferase activity by a newly developed small molecule, C646. Knockdown of p300 by specific siRNA, but surprisingly not of CBP, led to an increase of caspase-dependent apoptosis involving both extrinsic and intrinsic cell death pathways in androgen-dependent and castration-resistant prostate cancer cells. Induction of apoptosis was mediated by several pathways including inhibition of AR function and decrease of the nuclear factor kappa B (NF-κB) subunit p65. Furthermore, cell invasion was decreased upon p300, but not CBP, depletion and was accompanied by lower matrix metalloproteinase (MMP)-2 and MMP-9 transcriptions. Thus, p300 and CBP have differential roles in the processes of survival and invasion of prostate cancer cells. Induction of apoptosis in prostate cancer cells was confirmed by the use of C646. This was substantiated by a decrease of AR function and downregulation of p65 impairing several NF-κB target genes. Taken together, these results suggest that p300 inhibition may be a promising approach for the development of new anticancer therapies. Mol Cancer Ther; 10(9); 1644–55. ©2011 AACR.