Preimplantation genetic testing using Karyomapping for a paternally inherited reciprocal translocation: a case study.

Genome Scan for Therapy-Related Leukemia.

Objectives To determine the frequency of clinically significant chromosomal abnormalities identified by chromosomal microarray in pregnancy losses at any gestational age and to compare microarray performance with that of traditional cytogenetic analysis when testing pregnancy losses. Methods Among 535 fetal demise specimens of any gestational age, clinical microarray-based comparative genomic hybridization (aCGH) was performed successfully on 515, and a subset of 107 specimens underwent additional single nucleotide polymorphism (SNP) analysis. Results Overall, clinically significant abnormalities were identified in 12.8% (64/499) of specimens referred with normal or unknown karyotypes. Detection rates were significantly higher with earlier gestational age. In the subset with normal karyotype, clinically significant abnormalities were identified in 6.9% (20/288). This detection rate did not vary significantly with gestational age, suggesting that, unlike aneuploidy, the contribution of submicroscopic chromosomal abnormalities to fetal demise does not vary with gestational age. In the 107 specimens that underwent aCGH and SNP analysis, seven cases (6.5%) had abnormalities of potential clinical significance detected by the SNP component, including female triploidy. aCGH failed to yield fetal results in 8.3%, which is an improvement over traditional cytogenetic analysis of fetal demise specimens. Conclusions Both the provision of results in cases in which karyotype fails and the detection of abnormalities in the presence of a normal karyotype demonstrate the increased diagnostic utility of microarray in pregnancy loss. Thus, chromosomal microarray testing is a

Next-Generation Sequencing Is More Efficient at Detecting Mosaic Embryos and Improving Pregnancy Outcomes than Single-Nucleotide Polymorphism Array Analysis

Study question How do genetic centres in Belgium apply international guidelines on preimplantation genetic testing (PGT)? Summary answer We present the national consensus on how to practice PGT, starting from initial patient uptake and embryo selection to follow-up of pregnancies. What is known already PGT includes PGT-M for monogenic disorders, PGT-SR for structural rearrangements and PGT-A for aneuploidy screening. The application of whole-genome technologies to trophectoderm biopsies for PGT-M and PGT-SR/A has evidenced the high prevalence of mosaicism due to chromosome segregation errors during the first mitotic divisions, making biopsy results interpretation and embryo transfer policy more challenging and complex. Guidelines from several international societies have been published in recent years to leverage the standardization of the whole PGT service. Although these are based on expertise and continuously acquiring evidence, it is widely recognized that variations in local and national regulations diversify PGT practices. Study design, size, duration Recommendations regarding PGT indications, patient counselling, embryo transfer policy, reporting, quality and pregnancy follow-up have been built to harmonize PGT services nationally. With a special focus on mosaicism, aiming to balance the highest chance for a pregnancy with the lowest risk for a chromosomally abnormal ongoing pregnancy or child. Participants/materials, setting, methods The Belgian PGT working group consists of laboratory geneticists, clinical geneticists and IVF specialists from eight nationally accredited centres. The group operates under the BeSHG umbrella and meets quarterly to formulate opinions and statements on PGT practice with the main goal of guaranteeing a high standard of care, exchange knowledge and implement a harmonized workflow. The Belgian social security system provides reimbursement of six genetic testing cycles for all PGT-M/SR patients but not for PGT-A. Main results and the role of chance PGT is offered for all monogenic and chromosomal disorders, if the causal genetic variants are known and documented. PGT for HLA-typing is allowed for the therapeutic benefit of an existing child after couple's psychological evaluation. Aneuploidy screening can be offered to specific patient groups to increase IVF success rate. However, social sexing and testing for non-medical or eugenic purposes is prohibited. At intake, the couple is counselled about the genetic aspect of the disease, psychological and financial aspects of PGT, applied methodology, including average success and misdiagnosis rate, and embryo transfer policies. Affected embryos, and embryos without diagnosis for PGT-M/SR are not transferred. For PGT-A (combined or not with PGT-M/SR), embryos are categorized as: (A) Euploid - suitable for transfer, if mosaicism is absent or below the detection threshold. (B) Mosaic transferable - suitable for transfer, but only following ranking and/or counselling and follow up, if mosaicism for any chromosome not described in (C) is detected; (C) Aneuploid or Mosaic - not suitable for transfer, if mosaicism of 8, 9, 13, 16, 18, 21 and X or full aneuploidy of any chromosome is detected. Non-invasive prenatal testing is strongly recommended to all women pregnant after PGT and is nationally reimbursed. Limitations, reasons for caution The practical recommendations, which are supplementary to the recently published ESHRE PGT recommendations, are based on expertise and data from the literature available at the time of preparation. As such, they will need regular reconsideration and an update or extension may follow when new solid scientific evidence arises. Wider implications of the findings As international recommendations represent a greatest common denominator over many local regulations, this work serves as example for drawing country-specific agreements for genetic centres. The process of consensus expert opinion formation on best practice may be applicable in other countries where PGT service is not overseen by a designated agency. Trial registration number Not applicable

Our study established an effective next-generation sequencing (NGS) protocol for four-factor preimplantation genetic testing (PGT) using α- and β-thalassemia, human leukocyte antigen (HLA) typing, and aneuploidy screening. Three couples, in whom both partners were α- and β-double thalassemia carriers, underwent PGT between 2016 and 2018. These individuals sought an opportunity for hematopoietic stem cell transplantation to save their children from β-thalassemia major. A total of 35 biopsied trophectoderm samples underwent multiple displacement amplification (MDA). PGT for α- and β-thalassemia and HLA typing were performed on MDA products using NGS-based single-nucleotide polymorphism (SNP) haplotyping. Although two samples failed MDA, 94.3% (33/35) of samples were successfully amplified, achieving conclusive PGT results. Furthermore, 51.5% (17/33) of the embryos were diagnosed as unaffected non-carriers or carriers. Of the 17 unaffected embryos, nine (52.9%) were tested further and identified as euploid via NGS-based aneuploid screening, in which five had HLA types matching affected children. One family did not achieve any unaffected euploid embryos. The two other families transferred HLA-matched and unaffected euploid embryos, resulting in two healthy ‘savior babies.’ NGS-PGT results were confirmed in prenatal diagnosis. Therefore, NGS-SNP was effective in performing PGT for multipurpose detection within a single PGT cycle.

Enhanced precision of epidemiological typing in clinically suspected nosocomial outbreaks is crucial. Our aim was to investigate whether single nucleotide polymorphism (SNP) analysis and core genome (cg) multilocus sequence typing (MLST) of whole genome sequencing (WGS) data would more reliably identify a nosocomial outbreak, compared to earlier molecular typing methods. Sixteen isolates from a nosocomial outbreak of ESBL E.coli ST-131 in southeastern Sweden and three control strains were subjected to WGS. Sequences were explored by SNP analysis and cgMLST. cgMLST clearly differentiated between the outbreak isolates and the control isolates (>1400 differences). All clinically identified outbreak isolates showed close clustering (≥2 allele differences), except for two isolates (>50 allele differences). These data confirmed that the isolates with >50 differing genes did not belong to the nosocomial outbreak. The number of SNPs within the outbreak was ≤7, whereas the two discrepant isolates had >700 SNPs. Two of the ESBL E.coli ST-131 isolates did not belong to the clinically identified outbreak. Our results illustrate the power of WGS in terms of resolution, which may avoid overestimation of patients belonging to outbreaks as judged from epidemiological data and previously employed molecular methods with lower discriminatory ability.

452 Background: In ML18147, BEV + standard CT was continued as 2nd-line treatment for pts with mCRC progressing after 1st-line BEV + CT. ML18147 met its primary and secondary endpoints and had a comprehensive biomarker programme, including exploratory analyses of immunohistochemistry (IHC) and single nucleotide polymorphisms (SNPs). Methods: Tumour samples were analysed by IHC for VEGFA, VEGFR1, VEGFR2 and neuropilin-1; H-scores were generated. Tumor angiogenesis was determined by stereological analysis of CD31-stained microvessels; 183 SNPs of 30 mainly angiogenesis-related genes were genotyped. We assessed consistency of treatment effect point estimates, i.e. hazard ratios (HRs) on the same side of 1. Analyses were not adjusted for multiple testing or powered to detect statistically significant treatment by biomarker interactions. Results: IHC data were available for 213 pts (26% of ITT population) and SNP data for 274 pts (33% of ITT). There was no significant evidence of biomarker expression levels or their cellular localisation correlating with BEV treatment effect. Point estimates for a CD31 derivative (i.e. vessel or tumour area) suggested a trend for being predictive for overall survival (OS; HR 1.39 and 0.70 for CD31 derivative <median and ≥median, respectively), similar to data from previous studies. Other previously reported correlations (progression-free survival [PFS] with VEGFA and NRP1 in NO16966; OS with NRP1 in AVAGAST) were not seen. SNP analyses confirmed previous correlations for OS (VEGFA, VEGFR2) and suggested additional biomarker candidates (PFS: VEGFA, VEGFR1, VEGFR2, EGLN3; OS: VEGFR2, EGLN1). Five EPAS1 (HIF2α) SNPs were associated with BEV treatment effect, thus confirming previous findings of HIF2α SNPs as a predictive biomarker for BEV treatment effects. Conclusions: Exploratory IHC and SNP analyses in ML18147 revealed potential biomarker candidates for BEV in pts with mCRC. SNP analyses of angiogenesis-relevant genes were consistent with previous findings for a subset of SNPs, consolidating their role as potential predictive biomarkers of BEV treatment across indications. Clinical trial information: NCT00700102.

Preimplantation Genetic Testing (PGT) enables the genetic analysis of embryos generated through in vitro fertilization (IVF). Traditional applications of PGT include PGT for aneuploides (PGT-A - to identify whole-chromosome aneuploidies), PGT for structural rearrangements (PGT-SR - to detect chromosomal imbalances resulting from a balanced structural rearrangement, such as chromosomal translocations or inversions, in one of the patients), and PGT for monogenic disorders (PGT-M - to minimize the risk of transmitting a known inherited monogenic disorder). Recent advancements in Next Generation Sequencing (NGS) technologies used in PGT, combined with a substantial reduction in associated costs, have made Whole Genome Sequencing (WGS) a feasible approach at the embryonic level. This methodology provides genome-wide data, albeit typically at low coverage depth.These technological developments have enabled novel applications of PGT, such as screening embryos for monogenic variants (including de novo mutations) and polygenic embryo screening (PES). However, these approaches raise significant limitations and challenges, particularly from ethical and genetic counseling perspectives.This session will offer an overview of the key ethical and counseling dilemmas associated with the use of these emerging technologies, in order to facilitate a broader discussion on the scope and boundaries of PGT.

Deep impact: sequencing embryo biopsy specimens at increasing depth

Whole-genome analysis of a putative rare and complex interchromosomal reciprocal insertion: thorough investigations for a straightforward interpretation

Preimplantation genetic testing (PGT) involves testing embryos created through in vitro fertilization for the presence of hereditary genetic disorders and chromosome abnormalities. PGT for monogenic conditions (PGT-M) is generally performed for childhood-onset, lethal disorders, but is increasingly accepted for certain adult-onset conditions, conditions with available treatment options or conditions with lower penetrance. Furthermore, the development of PGT for polygenic conditions (PGT-P) makes ethical questions regarding PGT indications imperative. A systematic review was therefore performed to gather and analyse studies on the perspectives of healthcare professionals on the appropriate scope of PGT, with the aim of getting insights into the concerns about the scope of PGT now and in the near future. PRISMA guidelines were followed. Twelve qualitative articles were included. The main themes extracted were the scope of PGT and decision-making about PGT. Defining 'a serious genetic condition' was seen as complex, but severity, high penetrance and absence of treatability and patients' experience were seen as relevant indications to determine the appropriateness of PGT. In navigating the decision-making processes with patients, professionals experienced friction between setting limits and respecting patients' autonomy. Such friction and ethical dilemmas around seriousness, informed decision-making and preventative medicine show that while expanding the list of possible PGT indications and the development of PGT-P could augment patients' reproductive autonomy, it could also lead to an increased reproductive 'burden' for patients. These insights are crucial for establishing guidelines that help healthcare professionals navigate ethical tensions associated with PGT.

BackgroundSalmonella Typhimurium (STM) is an important cause of foodborne outbreaks worldwide. Subtyping of STM remains critical to outbreak investigation, yet current techniques (e.g. multilocus variable number tandem repeat analysis, MLVA) may provide insufficient discrimination. Whole genome sequencing (WGS) offers potentially greater discriminatory power to support infectious disease surveillance.MethodsWe performed WGS on 62 STM isolates of a single, endemic MLVA type associated with two epidemiologically independent, food-borne outbreaks along with sporadic cases in New South Wales, Australia, during 2014. Genomes of case and environmental isolates were sequenced using HiSeq (Illumina) and the genetic distance between them was assessed by single nucleotide polymorphism (SNP) analysis. SNP analysis was compared to the epidemiological context.ResultsThe WGS analysis supported epidemiological evidence and genomes of within-outbreak isolates were nearly identical. Sporadic cases differed from outbreak cases by a small number of SNPs, although their close relationship to outbreak cases may represent an unidentified common food source that may warrant further public health follow up. Previously unrecognised mini-clusters were detected.ConclusionsWGS of STM can discriminate foodborne community outbreaks within a single endemic MLVA clone. Our findings support the translation of WGS into public health laboratory surveillance of salmonellosis.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-016-0831-3) contains supplementary material, which is available to authorized users.

Personalized medicine for the embryo and the fetus - Options in modern genetics influence preconception and prenatal choices.

Background: Chromosomal abnormalities are the most common cause of recurrent abortions and miscarriages (RAM), but micro-variations on chromosomes causing RAM have never been previously studied. Single nucleotide polymorphisms (SNPs) are the single nucleotide variations frequently present at genome with the density of at least one common (>20% allele frequency) SNP per kilobase pair. It has already been reported that SNP array examination for chromosomal abnormalities has better performance than the conventional cytogenetic karyotyping.Methods: We applied SNP array to detect the chromosomal defects in 80 placental villi and foetal tissues of abnormal foetus and spontaneous abortions.Results: The analyses of data revealed that total 52.5% (42/80) cases were found to have chromosomal abnormalities. The trisomies were most commonly found 26/42 (61.9%) in current samples. Total 8/42 (19.1%) cases were found to have other structural aberrations including translocations in 2/8 (25%), duplications and deletions in 3/8 (37.5%) cases, respectively. SNP analysis also successfully detected triploidy 69,XXX and tetraploidy 92,XXXY. Total 12/80 cases were performed by cytogenetic karyotyping and results were compared with SNP data. Total 5/12 (41.7%) cases were found to have same findings with SNP data while results of 2/12 (16.7%) cases had partial similarity between both techniques. Four cases were declared as karyotypically normal (46,XY or 46,XX) by cytogenetic examination, but later on these four cases were found to have small chromosomal variation which could be the cause of RAM in women.Conclusion: Therefore, we conclude that use of a high-density SNP platform in diagnosis can give better understanding of molecular causes of pregnancy loss and foetal abnormalities.

Can whole genome sequencing (WGS) offer a relatively cost-effective approach for embryonic genome-wide haplotyping and preimplantation genetic testing (PGT) for monogenic disorders (PGT-M), aneuploidy (PGT-A) and structural rearrangements (PGT-SR)? Reliable genome-wide haplotyping, PGT-M, PGT-A and PGT-SR could be performed by WGS with 10× depth of parental and 4× depth of embryonic sequencing data. Reduced representation genome sequencing with a genome-wide next-generation sequencing haplarithmisis-based solution has been verified as a generic approach for automated haplotyping and comprehensive PGT. Several low-depth massively parallel sequencing (MPS)-based methods for haplotyping and comprehensive PGT have been developed. However, an additional family member, such as a sibling, or a proband, is required for PGT-M haplotyping using low-depth MPS methods. In this study, 10 families that had undergone traditional IVF-PGT and 53 embryos, including 13 embryos from two PGT-SR families and 40 embryos from eight PGT-M families, were included to evaluate a WGS-based method. There were 24 blastomeres and 29 blastocysts in total. All embryos were used for PGT-A. Karyomapping validated the WGS results. Clinical outcomes of the 10 families were evaluated. A blastomere or a few trophectoderm cells from the blastocyst were biopsied, and multiple displacement amplification (MDA) was performed. MDA DNA and bulk DNA of family members were used for library construction. Libraries were sequenced, and data analysis, including haplotype inheritance deduction for PGT-M and PGT-SR and read-count analysis for PGT-A, was performed using an in-house pipeline. Haplotyping with a proband and parent-only haplotyping without additional family members were performed to assess the WGS methodology. Concordance analysis between the WGS results and traditional PGT methods was performed. For the 40 PGT-M and 53 PGT-A embryos, 100% concordance between the WGS and single-nucleotide polymorphism (SNP)-array results was observed, regardless of whether additional family members or a proband was included for PGT-M haplotyping. For the 13 embryos from the two PGT-SR families, the embryonic balanced translocation was detected and 100% concordance between WGS and MicroSeq with PCR-seq was demonstrated. The number of samples in this study was limited. In some cases, the reference embryo for PGT-M or PGT-SR parent-only haplotyping was not available owing to failed direct genotyping. WGS-based PGT-A, PGT-M and PGT-SR offered a comprehensive PGT approach for haplotyping without the requirement for additional family members. It provided an improved complementary method to PGT methodologies, such as low-depth MPS- and SNP array-based methods. This research was supported by the research grant from the National Key R&D Program of China (2018YFC0910201 and 2018YFC1004900), the Guangdong province science and technology project of China (2019B020226001), the Shenzhen Birth Defect Screening Project Lab (JZF No. [2016] 750) and the Shenzhen Municipal Government of China (JCYJ20170412152854656). This work was also supported by the National Natural Science Foundation of China (81771638, 81901495 and 81971344), the National Key R&D Program of China (2018YFC1004901 and 2016YFC0905103), the Shanghai Sailing Program (18YF1424800), the Shanghai Municipal Commission of Science and Technology Program (15411964000) and the Shanghai 'Rising Stars of Medical Talent' Youth Development Program Clinical Laboratory Practitioners Program (201972). The authors declare no competing interests. N/A.