Whole exome sequencing of FFPE samples-expanding the horizon of forensic molecular autopsies.

Forensic molecular autopsies have emerged as a tool for medical examiners to establish the cause of death. It is particularly useful in sudden unexplained deaths where the cause of death cannot be determined with a regular medical autopsy. We provide the first study of exome data from formalin-fixed paraffin-embedded samples (FFPE) paired with data from high-quality blood samples in forensic applications. The approach allows exploration of the potential to use FFPE samples for molecular autopsies and identify variants in extensive exome data. We leverage the high uniformity of the hybridization capture approach provided by Twist Bioscience to target the complete exome and sequence the libraries on a NextSeq 550. Our findings suggest that exome sequencing is feasible for 24 out of a total of 35 included FFPE samples. When successful, the coverage across the exome is comparatively high (> 90% covered to 20X) and uniform (fold80 below 1.5). Detailed variant comparisons for matched FFPE and blood samples show high concordance with few false variants (positive predictive value of 0.98 and a sensitivity of 0.97) with no distinct FFPE artefacts. Ultimately, we apply carefully constructed forensic gene panels in a stepwise manner to find genetic variants associated with the clinical phenotype and with relevance to the sudden unexplained death.

Bone marrow- and adipose tissue-derived mesenchymal stem cells from donors with coronary artery disease; growth, yield, gene expression and the effect of oxygen concentration.

Mesenchymal stem cells (MSCs) for cardiovascular cell therapy are procured from different sources including bone marrow and adipose tissue. Differently located MSCs differ in growth potential, differentiation ability and gene expression when cultured in vitro, and studies show different healing abilities for different MSC subgroups. In this study, bone marrow derived MSCs (BMSCs) and adipose tissue derived MSCs (ADSCs) from six human donors with coronary artery disease were compared for growth potential and expression of target genes (Angpt1, LIF, HGF, TGF-ß1 and VEGF-A) in response to exposure to 1% and 5% O2, for up to 48 h. We found greater growth of ADSCs compared to BMSCs. ADSCs expressed higher levels of Angpt1, LIF and TGF-ß1 and equal levels of VEGF-A and HGF as BMSCs. In BMSCs, exposure to low oxygen resulted in upregulation of TGF-ß1, whereas other target genes were unaffected. Upregulation was only present at 1% O2. In ADSCs, LIF was upregulated in both oxygen concentrations, whereas Angpt1 was upregulated only at 1% O2. Different response to reduced oxygen culture conditions is of relevance when expanding cells in vitro prior to administration. These findings indicate ADSCs as better suited for cardiovascular cell therapy compared to BMSCs.

Technical in-depth comparison of two massive parallel DNA-sequencing methods for formalin-fixed paraffin-embedded tissue from victims of sudden cardiac death.

Sudden cardiac death (SCD) is a tragic and traumatic event. SCD is often associated with hereditary genetic disease and in such cases, sequencing of stored formalin fixed paraffin embedded (FFPE) tissue is often crucial in trying to find a causal genetic variant. This study was designed to compare two massive parallel sequencing assays for differences in sensitivity and precision regarding variants related to SCD in FFPE material. From eight cases of SCD where DNA from blood had been sequenced using HaloPlex, corresponding FFPE samples were collected six years later. DNA from FFPE samples were amplified using HaloPlex HS, sequenced on MiSeq, representing the first method, as well as amplified using modified Twist and sequenced on NextSeq, representing the second method. Molecular barcodes were included to distinguish artefacts from true variants. In both approaches, read coverage, uniformity and variant detection were compared using genomic DNA isolated from blood and corresponding FFPE tissue, respectively. In terms of coverage uniformity, Twist performed better than HaloPlex HS for FFPE samples. Despite higher overall coverage, amplicon-based HaloPlex technologies, both for blood and FFPE tissue, suffered from design and/or performance issues resulting in genes lacking complete coverage. Although Twist had considerably lower overall mean coverage, high uniformity resulted in equal or higher fraction of genes covered at ≥ 20X. By comparing variants found in the matched samples in a pre-defined cardiodiagnostic gene panel, HaloPlex HS for FFPE material resulted in high sensitivity, 98.0% (range 96.6-100%), and high precision, 99.9% (range 99.5-100%) for moderately fragmented samples, but suffered from reduced sensitivity (range 74.2-91.1%) in more severely fragmented samples due to lack of coverage. Twist had high sensitivity, 97.8% (range 96.8-98.7%) and high precision, 99.9% (range 99.3-100%) in all analyzed samples, including the severely fragmented samples.

External validation of a time-lapse model; a retrospective study comparing embryo evaluation using a morphokinetic model to standard morphology with live birth as endpoint.

OBJECTIVE: To validate a morphokinetic implantation model developed for EmbryoScope on embryos with known outcome, compared to standard morphology in a retrospective single center study. METHODS: Morphokinetic annotation of 768 embryos with known outcome between 2013 -2015; corresponding to 116 D3 fresh embryos, 80 D6 frozen blastocysts, and 572 D5 blastocysts, fresh or frozen. The embryos were ranked by the KIDScore into five classes, KID1-5, and grouped into four classes based on standard morphology. Pregnancy rates, clinical pregnancy rates and live birth rates were compared. Combinations of morphology and morphokinetics were evaluated for implantation rates and live births. RESULTS: Live birth rate increased with increasing KIDScore, from 19% for KID1 to 42% for KID5. Of all live births, KID5 contributed with 71%, KID4 with 20%, KID3 with 4%, KID2 with 4%, and KID1 with 2%. For morphology, the corresponding figure was 43% for Top Quality, 47% for Good Quality, 4% for Poor Quality, and 5% for Slow embryos. For day 3 embryos, KID5 embryos had the highest live birth rates, and contributed to 83% of the live births; whereas the second best morphological class had the highest live birth rate and contributed to most of the live births. For blastocysts, the KIDScore and morphology performed equally well. Combining morphology and morphokinetics indicated stronger predictive power for morphokinetics. CONCLUSIONS: Overall, the KIDScore correlates with both implantation and live birth in our clinical setting. Compared to morphology, the KIDScore was superior for day 3 embryos, and equally good for blastocysts at predicting live births.

Morphology vs morphokinetics: a retrospective comparison of inter-observer and intra-observer agreement between embryologists on blastocysts with known implantation outcome.

OBJECTIVE: Our primary aim was to compare the morphology and morphokinetics on inter- and intra-observer agreement for blastocyst with known implantation outcome. Our secondary aim was to validate the morphokinetic parameters' ability to predict pregnancy using a previous published selection algorithm, and to compare this to standard morphology assessments. METHODS: Two embryologists made independent blinded annotations on two occasions using time-lapse images and morphology evaluations using the Gardner Schoolcraft criteria of 99 blastocysts with known implantation outcome. Inter- and intra-observer agreement was calculated and compared using the two methods. The embryos were grouped based on their morphological score, and on their morphokinetic class using a previous published selection algorithm. The implantation rates for each group was calculated and compared. RESULTS: There was moderate agreement for morphology, with agreement on the same embryo score in 55 of 99 cases. The highest agreement rate was found for expansion grade, followed by trophectoderm and inner cell mass. Correlation with pregnancy was inconclusive. For morphokinetics, almost perfect agreement was found for early and late embryo development events, and strong agreement for day-2 and day-3 events. When applying the selection algorithm, the embryo distributions were uneven, and correlation to pregnancy was inconclusive. CONCLUSIONS: Time-lapse annotation is consistent and accurate, but our external validation of a previously published selection algorithm was unsuccessful.