A review of likelihood ratios in forensic science based on a critique of Stiffelman "No longer the Gold standard: Probabilistic genotyping is changing the nature of DNA evidence in criminal trials".

Stiffelman [1] gives a broad critique of the application of likelihood ratios (LRs) in forensic science, in particular their use in probabilistic genotyping (PG) software. These are discussed in this review. LRs do not infringe on the ultimate issue. The Bayesian paradigm clearly separates the role of the scientist from that of the decision makers and distances the scientist from comment on the ultimate and subsidiary issues. LRs do not affect the reasonable doubt standard. Fact finders must still make decisions based on all the evidence and they must do this considering all evidence, not just that given probabilistically. LRs do not infringe on the presumption of innocence. The presumption of innocence does not equate with a prior probability of zero but simply that the person of interest (POI) is no more likely than anyone else to be the donor. Propositions need to be exhaustive within the context of the case. That is, propositions deemed relevant by either defense or prosecution which are not fanciful must not be omitted from consideration.

STRmix™ collaborative exercise on DNA mixture interpretation.

An intra and inter-laboratory study using the probabilistic genotyping (PG) software STRmix™ is reported. Two complex mixtures from the PROVEDIt set, analysed on an Applied Biosystems™ 3500 Series Genetic Analyzer, were selected. 174 participants responded. For Sample 1 (low template, in the order of 200 rfu for major contributors) five participants described the comparison as inconclusive with respect to the POI or excluded him. Where LRs were assigned, the point estimates ranging from 2 × 104 to 8 × 106. For Sample 2 (in the order of 2000 rfu for major contributors), LRs ranged from 2 × 1028 to 2 × 1029. Where LRs were calculated, the differences between participants can be attributed to (from largest to smallest impact): This study demonstrates a high level of repeatability and reproducibility among the participants. For those results that differed from the mode, the differences in LR were almost always minor or conservative.

The Probabilistic Genotyping Software STRmix: Utility and Evidence for its Validity.

Forensic DNA interpretation is transitioning from manual interpretation based usually on binary decision-making toward computer-based systems that model the probability of the profile given different explanations for it, termed probabilistic genotyping (PG). Decision-making by laboratories to implement probability-based interpretation should be based on scientific principles for validity and information that supports its utility, such as criteria to support admissibility. The principles behind STRmix™ are outlined in this study and include standard mathematics and modeling of peak heights and variability in those heights. All PG methods generate a likelihood ratio (LR) and require the formulation of propositions. Principles underpinning formulations of propositions include the identification of reasonably assumed contributors. Substantial data have been produced that support precision, error rate, and reliability of PG, and in particular, STRmix™. A current issue is access to the code and quality processes used while coding. There are substantial data that describe the performance, strengths, and limitations of STRmix™, one of the available PG software.

Microscopy and Image Analysis.

This unit provides an overview of light microscopy, including objectives, light sources, filters, film, and color photography for fluorescence microscopy and fluorescence in situ hybridization (FISH). We believe there are excellent opportunities for cytogeneticists, pathologists, and other biomedical readers, to take advantage of specimen optical clearing techniques and expansion microscopy-we briefly point to these new opportunities. © 2017 by John Wiley & Sons, Inc.

A new diagnosis of Williams-Beuren syndrome in a 49-year-old man with severe bullous emphysema.

Williams-Beuren syndrome (WBS) is a chromosomal microdeletion syndrome typically presenting with intellectual disability, a unique personality, a characteristic facial appearance, and cardiovascular disease. Several clinical features of WBS are thought to be due to haploinsufficiency of elastin (ELN), as the ELN locus is included within the WBS critical region at 7q11.23. Emphysema, a disease attributed to destruction of pulmonary elastic fibers, has been reported in patients without WBS who have pathogenic variants in ELN but only once (in one patient) in WBS. Here we report a second adult WBS patient with emphysema where the diagnosis of WBS was established subsequent to the discovery of severe bullous emphysema. Haploinsufficiency of ELN likely contributed to this pulmonary manifestation of WBS. This case emphasizes the contribution of rare genetic variation in cases of severe emphysema and provides further evidence that emphysema should be considered in patients with WBS who have respiratory symptoms, as it may be under-recognized in this patient population.

Commentary on the decision of the American Board of Medical Genetics and Genomics to create a 24-month specialty of Laboratory Genetics and Genomics.

Genet Med 19 3, 294-296.

Evaluation of forensic DNA mixture evidence: protocol for evaluation, interpretation, and statistical calculations using the combined probability of inclusion.

BACKGROUND: The evaluation and interpretation of forensic DNA mixture evidence faces greater interpretational challenges due to increasingly complex mixture evidence. Such challenges include: casework involving low quantity or degraded evidence leading to allele and locus dropout; allele sharing of contributors leading to allele stacking; and differentiation of PCR stutter artifacts from true alleles. There is variation in statistical approaches used to evaluate the strength of the evidence when inclusion of a specific known individual(s) is determined, and the approaches used must be supportable. There are concerns that methods utilized for interpretation of complex forensic DNA mixtures may not be implemented properly in some casework. Similar questions are being raised in a number of U.S. jurisdictions, leading to some confusion about mixture interpretation for current and previous casework. RESULTS: Key elements necessary for the interpretation and statistical evaluation of forensic DNA mixtures are described. Given the most common method for statistical evaluation of DNA mixtures in many parts of the world, including the USA, is the Combined Probability of Inclusion/Exclusion (CPI/CPE). Exposition and elucidation of this method and a protocol for use is the focus of this article. Formulae and other supporting materials are provided. CONCLUSIONS: Guidance and details of a DNA mixture interpretation protocol is provided for application of the CPI/CPE method in the analysis of more complex forensic DNA mixtures. This description, in turn, should help reduce the variability of interpretation with application of this methodology and thereby improve the quality of DNA mixture interpretation throughout the forensic community.

Reporting of Diagnostic Cytogenetic Results.

This appendix, developed by the staff at the Center for Advanced Molecular Diagnostics in the Department of Pathology at the Brigham and Women's Hospital, includes a comprehensive list of current "macros" or standardized statements used to facilitate reporting of cytogenetic results. These are provided as a useful reference for other laboratories. The statements are organized under the general categories of constitutional or acquired abnormalities and subdivided into analysis type (GTG-banding, FISH, or chromosomal microarray). Multi-specimen usage macros are included that can be applied to two or more specimen types.

Reporting of diagnostic cytogenetic results.

This appendix, developed by the staff at the Clinical Cytogenetics Laboratory at the Brigham and Women's Hospital, includes a comprehensive list of current "macros" or standardized statements used to facilitate reporting of cytogenetic results. These are provided as a reference for other laboratories. The statements are organized under the general categories of constitutional or acquired abnormalities and subdivided into analysis type (GTG-banding or FISH). Multi-specimen usage macros are included that can be applied to two or more specimen types.

Reporting of diagnostic cytogenetic results.

This appendix, developed by the staff at the Clinical Cytogenetics Laboratory at the Brigham and Women's Hospital, includes a comprehensive list of current "macros" or standardized statements used to facilitate reporting of cytogenetic results. These are provided as a reference for other laboratories. The statements are organized under the general categories of constitutional or acquired abnormalities and subdivided into analysis type (GTG-banding or FISH). Multi-specimen usage macros are included that can be applied to two or more specimen types.

Epidemiology. DNA identifications after the 9/11 World Trade Center attack.

The attack on the World Trade Center on 9/11/2001 challenged current approaches to forensic DNA typing methods. The large number of victims and the extreme thermal and physical conditions of the site necessitated special approaches to the DNA-based identification. Because of these and many additional challenges, new procedures were created or modified from routine forensic protocols. This effort facilitated the identification of 1594 of the 2749 victims. In this Policy Forum, the authors, who were were members of the World Trade Center Kinship and Data Analysis Panel, review the lessons of the attack response from the perspective of DNA forensic identification and suggest policies and procedures for future mass disasters or large-scale terrorist attacks.

Forensic applications of laser capture microdissection: use in DNA-based parentage testing and platform validation.

AIM: To report on the successful use of Laser Capture Microdissection (LCM) as a tool for isolation of human chorionic villi from admixed maternal tissue. Subsequent DNA isolation for forensic short tandem repeat (STR) analysis for parentage testing was performed in two cases of alleged sexual assault of female victims. We also performed validation of the LCM instrument platform, using archival formalin-fixed human fetal products of conception (POC), for which microdissection was utilized to separate maternal (decidua) and fetal (chorionic villus) components. METHODS: To isolate DNA from placental chorionic villi admixed with maternal decidua recovered after spontaneous or therapeutic abortion, LCM was used to separate fetal from maternal cells. In contrast to the relatively crude conventional microdissection performed using a narrow pipette, needle, or scalpel blade, LCM allows cell- or tissue-specific isolation of placental chorionic villi from archival paraffin-embedded tissue sections, leaving the maternal tissue intact. RESULTS: After polymerase chain reaction (PCR) amplification of villi after LCM of 9-15 STR loci, the quantity and quality of DNA yielded from fetal cells isolated by LCM was sufficient for PCR analysis and successful forensic parentage testing. The validation data obtained on two sets of formalin-fixed archival POC tissues from anonymous donors demonstrated the encouraging reproducibility of these protocols and procedures. CONCLUSION: We demonstrated the reliability and utility of LCM for forensic applications when high specificity of a particular analyzed cell population or tissue is required. Care must be taken during routine pathology procedures to avoid contamination of tissues with admixture of extraneous DNA.

Forensic aspects of mass disasters: strategic considerations for DNA-based human identification.

Many mass disasters result in loss of lives. Law enforcement and/or public safety and health officials often have the responsibility for identifying the human remains found at the scene, so they can be returned to their families. The recovered human remains range from being relatively intact to highly degraded. DNA-based identity testing is a powerful tool for victim identification in that the data are not restricted to any particular one to one body landmark comparison and DNA profile comparisons can be used to associate separated remains or body parts. Even though DNA typing is straightforward, a disaster is a chaotic environment that can complicate effective identification of the remains. With some planning, or at least identification of the salient features to consider, stress can be reduced for those involved in the identification process. General guidelines are provided for developing an action plan for identification of human remains from a mass disaster by DNA analysis. These include: (1) sample collection, preservation, shipping and storage; (2) tracking and chain of custody issues; (3) laboratory facilities; (4) quality assurance and quality control practices; (5) parsing out work; (6) extraction and typing; (7) interpretation of results; (8) automation; (9) software for tracking and managing data; (10) the use of an advisory panel; (11) education and communication; and (12) privacy issues. In addition, key technologies that may facilitate the identification process are discussed, such as resin based DNA extraction, real-time PCR for quantitation of DNA, use of mini-STRs, SNP detection procedures, and software. Many of the features necessary for DNA typing of human remains from a mass disaster are the same as those for missing persons' cases. Therefore, developing a missing persons DNA identification program would also provide the basis for a mass disaster human remains DNA identification program.

Reporting of diagnostic cytogenetic results.

This appendix, developed by the staff at the Clinical Cytogenetics Laboratory at the Brigham and Women's Hospital, provides a comprehensive list of the facilities' current "macros" or standardized statements, used to facilitate reporting of cytogenetic results. These are provided as a reference for other laboratories. The statements are organized under the general categories of constitutional or acquired abnormalities and subdivided into analysis type (GTG-banding or FISH). Multi-specimen usage macros are included that can be applied to two or more specimen types.