Donor-derived, metastatic urothelial cancer after kidney transplantation associated with a potentially oncogenic BK polyomavirus.

BK polyomavirus has been linked to urothelial carcinoma in immunosuppressed patients. Here, we performed comprehensive genomic analysis of a BK polyomavirus-associated, metachronous, multifocal and metastatic micropapillary urothelial cancer in a kidney transplant recipient. Dissecting cancer heterogeneity by sorting technologies prior to array-comparative genomic hybridization followed by short tandem repeat analysis revealed that the metastatic urothelial cancer was of donor origin (4-year-old male). The top 50 cancer-associated genes showed no key driver mutations as assessed by next-generation sequencing. Whole genome sequencing and BK polyomavirus-specific amplification provided evidence for episomal and subgenomic chromosomally integrated BK polyomavirus genomes, which carried the same unique 17-bp deletion signature in the viral non-coding control region (NCCR). Whereas no role in oncogenesis could be attributed to the host gene integration in chromosome 1, the 17-bp deletion in the NCCR increased early viral gene expression, but decreased viral replication capacity. Consequently, urothelial cells were exposed to high levels of the transforming BK polyomavirus early proteins large tumour antigen and small tumour antigen from episomal and integrated gene expression. Surgery combined with discontinuation of immunosuppression resulted in complete remission, but sacrificed the renal transplant. Thus, this report links, for the first time, BK polyomavirus NCCR rearrangements with oncogenic transformation in urothelial cancer in immunosuppressed patients. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

A global analysis of Y-chromosomal haplotype diversity for 23 STR loci.

In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.

Allelic proportions of 16 STR loci-including the new European Standard Set (ESS) loci-in a Swiss population sample.

Allele frequencies and forensically relevant population statistics of 16 STR loci, including the new European Standard Set (ESS) loci, were estimated from 668 unrelated individuals of Caucasian appearance living in different parts of Switzerland. The samples were amplified with a combination of the following three kits: AmpFlSTR® NGM SElect™, PowerPlex® ESI17 and PowerPlex® ESX 17. All loci were highly polymorphic and no significant departure from Hardy-Weinberg equilibrium and linkage equilibrium was detected after correction for sampling.

[Fixation of cells for analysis by laser microdissection--comparative studies in forensic trace material]. / Fixierung von Zellen zur Analyse mittels Laser-Mikrodissektion: Vergleichende Untersuchungen an forensischem Spurenmaterial.

This paper is focused on the preparation of samples for laser microdissection (LM) in forensic casework. In forensic genetics, it is essential to preserve and separate cellular traces during sample preparation, as they are usually gathered in very small amounts and are often contaminated with undesired cells. This is made possible by laser microdissection, a technique developed to cut cells or tissue of a certain type from a microscopical specimen by UV laser and catapult them directly into a PCR reactor. This method minimizes the risk of getting inconclusive, mixed DNA profiles due to contamination by foreign DNA and also supplies information about the cellular origin of a DNA profile. A method for optimized fixation and staining of spermatozoa for laser microdissection was established. Four different fixation methods combined with two staining methods were tested on two different microscope slides. Moreover, the effect of a blocker pen to contain the specimen on the slide was investigated.

[Analysis with the Combur-Test--special aspects in forensic trace examination]. / Analysen mit dem Combur-test--Besonderheiten in der forensischen Spurenuntersuchung.

The Combur Test is a ready-made and easy-to-use pretest for blood. It is based on the oxidation of tetramethylbenzidine (TMB), which is catalysed by haemoglobin and its derivatives. Despite its high sensitivity, there are many known substances which are responsible for false positive and false negative test results. On the basis of experiments of our own, case reports and the pertinent literature special aspects of the application of the Combur Test in the forensic routine case work are discussed.

[Identification of a corpse using autosomal and gonosomal STR markers]. / Identifikation einer Leiche mithilfe autosomaler und gonosomaler STR-marker.

The identification of unidentified corpses poses an exceptional challenge in the field of forensic medicine, because visual traits are often unspecific. Forensic genetics offer a reliable means to determine the identity of a corpse unambiguously. In the process, Y and X chromosomal markers play an important role. Here, we report about a case out of the ordinary where a corpse was properly identified using forensic genetic methods.

Method to predict the chance of developing a male profile out of mixtures of male and female DNA.

In forensic examination it is a standard to take vaginal swabs from victims of sexual assault for further molecular genetic analysis. Laboratories then are usually confronted with mixtures of lots of female and only a small amount of male DNA. Nowadays it is possible to work with specific Y chromosomal markers after DNA extraction by differential lysis. The determined ratio of autosomal DNA and Y chromosomal DNA can be used to identify the possibility of generating a male profile in these samples.

[Recovery of blood traces with scenesafe FAST tape]. / Sicherung von Blutspuren mit Scenesafe FAST Tape.

For complete and conclusive DNA profiling a sufficient amount of DNA must be available. For that, biological traces are recovered from crime scenes using special trace recovery material. The current method to collect biological traces for DNA analysis is to wipe them off with cotton swabs. However, for a few years the use of adhesive tapes has also been described for the recovery of evidence. In 2009, an adhesive tape was launched which was specially developed for the collection of biological traces. This product called Scenesafe FAST Tape (SSF) was investigated in this work to give recommendations for its use in evidence recovery. The results of this work show that the DNA can be extracted from the SSF very well. However, the tapes seem less suitable for direct use at the crime scene, as they are not flexible enough for adaptation to different crime scene conditions and the risk of contamination is higher than when collecting evidence with cotton swabs. Neither SSF nor cotton swabs are optimal for all requirements. The best method to recover biological evidence is still dependent on the surface material and the circumstances at the crime scene.

[Semen analysis using methods of molecular genetics--a case report]. / Anwendung des molekulargenetischen Spermanachweises--ein Fallbeispiel.

The presented case report describes the exclusion of the suspect of a sexual offence by means of methods of molecular genetics. Pretests for prostate-specific antigen performed at the beginning of the investigation and cytological sperm tests were negative. Nevertheless, by combining the methods of differential lysis and DNA quantification a small number of spermatozoa could be demonstrated in the trace evidence. Subsequently, the profile of the woman's boyfriend, with whom she had had unprotected vaginal intercourse two days before the incident, could be detected in the fraction of the hard lysis.

[Reconstruction of sexual offences--forensic aspects of sperm traces]. / Tatrekonstruktion bei Sexualdelikten--forensische Aspekte von Spermaspuren.

The investigation of sexual offences is a real challenge, as the injuries are often unspecific or faint and may sometimes be missing completely. Evidence recovery and analysis as well as the statements of the victims and suspects are therefore of vital importance. In both presented cases, the results of trace evidence analysis were basically consistent with a sexual assault, but the victims' statements regarding the course of events and the pattern of traces showed severe discrepancies.