Whole genome sequencing of hematologically stained cells catapulted from Cell smears

Analyzing archived peripheral blood smears is a potential route towards gaining cell morphology and genome information of blood cell types from various diseases. Yet, acquiring whole genome information from morphologically targeted cells was difficult, especially for rare cell types. The main causes for such difficulty were the inevitable usage of cell stains leading to whole genome amplification inhibition, and insufficient cell isolation performance of previously introduced laser microdissection (LMD) techniques. Here, we introduce a new laser-based cell isolation technique and a whole genome amplification (WGA) protocol optimized for whole genome analysis from minute input of hematologically stained cells. We were able to perform whole genome copy number profiling and SNP analysis from as little as 5 cells.

Hiệu quả kết hợp chẩn đoán và sàng lọc di truyền tiền làm tổ trên phôi của bệnh teo cơ tủy

Mục tiêu: Đánh giá hiệu quả kết hợp chẩn đoán và sàng lọc nhiễm sắc thể trên phôi tiền làm tổ của bệnh teo cơ tủy (spinal muscular atrophy – SMA). Đối tượng và phương pháp: 11 cặp vợ chồng có tiền sử sinh con bị bệnh SMA do mất đồng hợp tử exon 7 gen SMNt tham gia làm thụ tinh ống nghiệm. Phương pháp nghiên cứu: Kích thích buồng trứng có kiểm soát, tạo phôi nuôi đến giai đoạn phôi nang. Sinh thiết các tế bào lá nuôi để làm vật liệu di truyền dùng cho chẩn đoán bằng 2 kỹ thuật PCR-RFLP và minisequensing. Phôi không bị bệnh tiến hành sàng lọc bất thường nhiễm sắc thể trên mẫu WGA (whole genome amplification) bằng giải trình tự gen thế hệ mới NGS (next generation genetic sequensing). Phôi không bị mất đồng hợp exon 7 gen SMNt gây bệnh teo cơ tủy và bình thường nhiễm sắc thể sẽ được chuyển phôi ở chu kỳ sau đó. Kết quả: 49 số phôi nang đủ tiêu chuẩn sinh thiết để thực hiện PGT-M và PGT-A, trong đó có 17 phôi mất đồng hợp tử exon 7 gen SMNt gây bệnh SMA) (34,7%), (32 phôi không bị mất exon 7 gen SMNt nên không gây bệnh SMA). 32 phôi không mắc bệnh SMA được làm sàng lọc (PGT-A) có 20 phôi chuẩn bội (62,5%). 10 gia đình được chuyển một phôi bình thường trong chu kỳ chuyển phôi trữ sau đó, 6 phụ nữ chuyển phôi thành công với tỷ lệ thai lâm sàng 60% (6/10), tỷ lệ phôi làm tổ 60% (6/10), 6 em bé sinh ra khỏe mạnh. Kết luận: PGT-M kết hợp với PGT-A sẽ chọn lựa phôi khỏe, cải thiện tỷ lệ có thai và sinh ra các bé khỏe mạnh.

Hepatocyte Polyploidy: Driver or Gatekeeper of Chronic Liver Diseases

Polyploidy, also known as whole-genome amplification, is a condition in which the organism has more than two basic sets of chromosomes. Polyploidy frequently arises during tissue development and repair, and in age-associated diseases, such as cancer. Its consequences are diverse and clearly different between systems. The liver is a particularly fascinating organ in that it can adapt its ploidy to the physiological and pathological context. Polyploid hepatocytes are characterized in terms of the number of nuclei per cell (cellular ploidy; mononucleate/binucleate hepatocytes) and the number of chromosome sets in each nucleus (nuclear ploidy; diploid, tetraploid, octoploid). The advantages and disadvantages of polyploidy in mammals are not fully understood. About 30% of the hepatocytes in the human liver are polyploid. In this review, we explore the mechanisms underlying the development of polyploid cells, our current understanding of the regulation of polyploidization during development and pathophysiology and its consequences for liver function. We will also provide data shedding light on the ways in which polyploid hepatocytes cope with centrosome amplification. Finally, we discuss recent discoveries highlighting the possible roles of liver polyploidy in protecting against tumor formation, or, conversely, contributing to liver tumorigenesis.

SureTypeSCR: R package for rapid quality control and genotyping of SNP arrays from single cells

Genotyping of single cells using single nucleotide polymorphism arrays is a cost-effective technology that provides good coverage and precision, but requires whole genome amplification (WGA) due to the low amount of genetic material. Since WGA introduces noise, we recently developed SureTypeSC, an algorithm to minimize genotyping errors. Here, we present SureTypeSCR, an R package that integrates a state-of-the-art algorithm (SureTypeSC) for noise reduction in single cell genotyping and unites all common parts of genotyping workflow in a single tool. SureTypeSCR is built on top of the tidyverse ecosystem, which facilitates common operations over the data and allows users to create and experiment with the genotyping pipeline. Furthermore, the workflow of SureTypeSCR can also be used for standard genotyping of bulk DNA for batch processing in a single pipeline. SureTypeSCR is avaliable from: https://github.com/Meiomap/SureTypeSCR

Comparison of seven single cell whole genome amplification commercial kits using targeted sequencing

Advances in whole genome amplification (WGA) techniques enable understanding of the genomic sequence at a single cell level. Demand for single cell dedicated WGA kits (scWGA) has led to the development of several commercial kit. To this point, no robust comparison of all available kits was performed. Here, we benchmark an economical assay, comparing all commercially available scWGA kits. Our comparison is based on targeted sequencing of thousands of genomic loci, including highly mutable regions, from a large cohort of human single cells. Using this approach we have demonstrated the superiority of Ampli1 in genome coverage and of RepliG in reduced error rate. In summary, we show that no single kit is optimal across all categories, highlighting the need for a dedicated kit selection in accordance with experimental requirements.