Implementing a biogeographic ancestry inference service for forensic casework.

The Centre of Forensic Sciences has validated the Precision ID Ancestry Panel on the Ion S5™ Massively Parallel Sequencing instrument for use in forensic casework. The focus of this paper is the development of reporting guidelines for implementation of the biogeographic ancestry inference service based on the Admixture Prediction results produced using the Torrent Suite™ Software (Thermo Fisher Scientific). The Admixture Prediction algorithm estimates the genetic ancestry of a sample using seven root populations (Europe, East Asia, Oceania, America, Africa, South Asia, and Southwest Asia). For individuals that declared a single ancestry, there was a high correlation between the declared ancestry and the ancestry predicted by the algorithm. However, some individuals with declared ancestries of Southern Europe, Southwest Asia, South Asia and Horn of Africa had Admixture Predictions that were composed of two or more root populations at 20% or greater. For individuals with known admixed ancestry, the major component of their declaration was included in their results in all but one case. Based on these results, reporting guidelines were developed and subsequently evaluated using the Admixture Predictions of additional samples. This paper discusses the development and evaluation of these reporting guidelines, along with an implementation plan for forensic casework.

Concentrating forensic DNA sample extracts on the Microlab® STARlet using the Microlab® monitored multi-flow, positive pressure, evaporative extraction module unit.

A Microlab® Monitored Multi-Flow, Positive Pressure, Evaporative Extraction module ([MPE]2) unit (Hamilton Company, Reno, Nevada, USA) was installed on the Microlab® STARlet Automated Liquid Handler (Hamilton Company, Reno, Nevada, USA) to add sample concentrating capabilities to the Centre of Forensic Sciences' automated workflow. Prior to incorporation of the [MPE]2, forensic samples extracted on the STARlet that required concentration to meet the CFS' amplification threshold were not amplified. Filtering parameters were first optimized, then contamination was assessed, and mock casework studies were completed. There was no evidence of cross contamination or sample loss during sample concentration on the [MPE]2. Extracts from blood, envelope flaps, cigarette butts and drink container swabs were concentrated using the [MPE]2 and amplified using AmpFLSTR™ Identifiler™ Plus (Applied Biosystems™). Profiles were concordant with similar peak heights, whether concentrated manually or with the [MPE]2. Post validation, the [MPE]2 was successfully introduced into casework and in the first year an additional 450 DNA profiles, which previously would not have been amplified, were uploaded to Canada's National DNA Databank.

Drosophila melanogaster Cad99C, the orthologue of human Usher cadherin PCDH15, regulates the length of microvilli.

Actin-based protrusions can form prominent structures on the apical surface of epithelial cells, such as microvilli. Several cytoplasmic factors have been identified that control the dynamics of actin filaments in microvilli. However, it remains unclear whether the plasma membrane participates actively in microvillus formation. In this paper, we analyze the function of Drosophila melanogaster cadherin Cad99C in the microvilli of ovarian follicle cells. Cad99C contributes to eggshell formation and female fertility and is expressed in follicle cells, which produce the eggshells. Cad99C specifically localizes to apical microvilli. Loss of Cad99C function results in shortened and disorganized microvilli, whereas overexpression of Cad99C leads to a dramatic increase of microvillus length. Cad99C that lacks most of the cytoplasmic domain, including potential PDZ domain-binding sites, still promotes excessive microvillus outgrowth, suggesting that the amount of the extracellular domain determines microvillus length. This study reveals Cad99C as a critical regulator of microvillus length, the first example of a transmembrane protein that is involved in this process.

Expression profile of the cadherin family in the developing Drosophila brain.

The Drosophila genome encodes 17 members of the cadherin family of adhesion molecules, which in vertebrates has been implicated in patterning the nervous system through cell and axon sorting. With only a few exceptions all cadherins show widespread expression in the larval brain. What expression patterns have in common is that 1) they are global, in the sense that all lineages of the central brain or optic lobe, or both, show expression; and 2) expression is stage-specific: some cadherins are expressed only in primary neurons (located closest to the neuropile), others in early secondary neurons (near the brain surface), or primaries plus late secondaries. The Fat-like cadherins, Fat and Dachsous, as well as Cad96Ca and Cad74A, are expressed in the epithelial optic lobe anlagen, which matches the widespread epithelial expression of these molecules in the embryo. DE-cadherin is restricted to immature secondary neurons and glia; by contrast, DN-cadherin, Flamingo, Cad87A, Cad99C, and Calsyntenin-1 appear in differentiating primary neurons and, at a later stage, some or all secondary neurons. Cad87A is strongly enriched apically in epithelia and in neuronal dendrites. Fat-like, Cad86C, Cad88C, Cad89D, and Dret are expressed ubiquitously in embryonic and larval brains at low or moderate levels. We conclude from this analysis that cadherins are likely to play a role in 'generic' neural functions, such as neurite fasciculation, branching, and synapse formation.

Genetic variation at the calcium-sensing receptor (CASR) locus: implications for clinical molecular diagnostics.

OBJECTIVES: The calcium-sensing receptor (CASR) is critical for maintenance of blood calcium in a narrow physiologic range. Naturally occurring mutations in the calcium-sensing receptor gene (CASR) cause hypocalcaemia or hypercalcaemia, and molecular diagnosis of these mutations is clinically important. Knowledge of SNP frequency and haplotype structure is essential in understanding molecular test results. DESIGN AND METHODS: Genotyping and haplotype analysis of 26 CASR SNPs (and a tetranucleotide insertion/deletion polymorphism) in control cohorts of Caucasian, Asian and African-American origin (n=1136, 88 and 104 chromosomes, respectively). RESULTS: The three SNPs in exon 7 (A986S, R990G, Q1011E) are the only common exonic variants in our cohorts, and synonymous exonic SNPs are uncommon. Linkage disequilibrium analysis of the Caucasian cohort (Haploview) showed that the CASR locus is divided into three haplotype blocks, coincident with 5' regulatory, coding, and 3' regulatory domains. CONCLUSIONS: These analyses provide an important framework for appropriate interpretation of CASR mutation screening now offered by a number of laboratories for the diagnosis of calcium disorders. They will assist in the study of CASR polymorphisms as predictors of complex disease states.