Single-Cell Genetic Analysis Using Automated Microfluidics to Resolve Somatic Mosaicism

Somatic mosaicism occurs throughout normal development and contributes to numerous disease etiologies, including tumorigenesis and neurological disorders. Intratumor genetic heterogeneity is inherent to many cancers, creating challenges for effective treatments. Unfortunately, analysis of bulk DNA masks subclonal phylogenetic architectures created by the acquisition and distribution of somatic mutations amongst cells. As a result, single-cell genetic analysis is becoming recognized as vital for accurately characterizing cancers. Despite this, methods for single-cell genetics are lacking. Here we present an automated microfluidic workflow enabling efficient cell capture, lysis, and whole genome amplification (WGA). We find that ~90% of the genome is accessible in single cells with improved uniformity relative to current single-cell WGA methods. Allelic dropout (ADO) rates were limited to 13.75% and variant false discovery rates (SNV FDR) were 4.11x10^-6, on average. Application to ER-/PR-/HER2+ breast cancer cells and matched normal controls identified novel mutations that arose in a subpopulation of cells and effectively resolved the segregation of known cancer-related mutations with single-cell resolution. Finally, we demonstrate effective cell classification using mutation profiles with 10X average exome coverage depth per cell. Our data demonstrate an efficient automated microfluidic platform for single-cell WGA that enables the resolution of somatic mutation patterns in single cells.     

Parental Somatic Mosaicism Is Underrecognized and Influences Recurrence Risk of Genomic Disorders

New human mutations are thought to originate in germ cells, thus making a recurrence of the same mutation in a sibling exceedingly rare. However, increasing sensitivity of genomic technologies has anecdotally revealed mosaicism for mutations in somatic tissues of apparently healthy parents. Such somatically mosaic parents might also have germline mosaicism that can potentially cause unexpected intergenerational recurrences. Here, we show that somatic mosaicism for transmitted mutations among parents of children with simplex genetic disease is more common than currently appreciated. Using the sensitivity of individual-specific breakpoint PCR, we prospectively screened 100 families with children affected by genomic disorders due to rare deletion copy-number variants (CNVs) determined to be de novo by clinical analysis of parental DNA. Surprisingly, we identified four cases of low-level somatic mosaicism for the transmitted CNV in DNA isolated from parental blood. Integrated probabilistic modeling of gametogenesis developed in response to our observations predicts that mutations in parental blood increase recurrence risk substantially more than parental mutations confined to the germline. Moreover, despite the fact that maternally transmitted mutations are the minority of alleles, our model suggests that sexual dimorphisms in gametogenesis result in a greater proportion of somatically mosaic transmitting mothers who are thus at increased risk of recurrence. Therefore, somatic mosaicism together with sexual differences in gametogenesis might explain a considerable fraction of unexpected recurrences of X-linked recessive disease. Overall, our results underscore an important role for somatic mosaicism and mitotic replicative mutational mechanisms in transmission genetics.     

Skewed X-Chromosome Inactivation Is Common in Fetuses or Newborns Associated with Confined Placental Mosaicism

The inactivation of one X chromosome in females is normally random with regard to which X is inactivated. However, exclusive or almost-exclusive inactivation of one X may be observed in association with some X-autosomal rearrangements, mutations of the XIST gene, certain X-linked diseases, and MZ twinning. In the present study, a methylation difference near a polymorphism in the X-linked androgen-receptor gene was used to investigate the possibility that nonrandom X inactivation is increases in fetuses and newborns that are associated with confined placental mosaicism (CPM) involving an autosomal trisomy. Extreme skewing was observed in 7 (58%) of 12 cases with a meiotic origin of the trisomy, but in none of 10 cases examined with a somatic origin of the trisomy, and in only 1 (4%) of 27 control adult females. In addition, an extremely skewed X-inactivation pattern was observed in 3 of 10 informative cases of female uniparental disomy (UPD) of chromosome 15. This may reflect the fact that a proportion of UPD cases arise by "rescue" of a chromosomally abnormal conceptus and are therefore associated with CPM. A skewed pattern of X inactivation in CPM cases is hypothesized to result from a reduction in the size of the early-embryonic cell pool, because of either poor early growth or subsequent selection against the trisomic cells. Since approximately 2% of pregnancies detected by chorionic villus sampling are associated with CPM, this is likely a significant contributor to both skewed X inactivation observed in the newborn population and the expression of recessive X-linked diseases in females.     

Mosaicism in mammals

Summary Eighteen new cases of colour mosaics are described. Previous reports of mosaics are collocated and briefly discussed. Various mechanisms are described which may engender three types of mosaicism. These are the (1) somatic, (2) the soma-gonadic and (3) the gonadic. The first type is the most frequent but representatives of the other two types are not unknown. The analytical study of both spontaneous and induced mosaicism holds promise for the study of cell lineage and tissue dynamics. A possible tendency of white spotting to act as an organiser is noted. The usefulness of the study of mosaicism for analysis of complex loci is touched upon.     

Porcine Model of Hemophilia A

Hemophilia A is a common X chromosome-linked genetic bleeding disorder caused by abnormalities in the coagulation factor VIII gene (F8). Hemophilia A patients suffer from a bleeding diathesis, such as life-threatening bleeding in the brain and harmful bleeding in joints and muscles. Because it could potentially be cured by gene therapy, subhuman animal models have been sought. Current mouse hemophilia A models generated by gene targeting of the F8 have difficulties to extrapolate human disease due to differences in the coagulation and immune systems between mice and humans. Here, we generated a porcine model of hemophilia A by nuclear transfer cloning from F8-targeted fibroblasts. The hemophilia A pigs showed a severe bleeding tendency upon birth, similar to human severe hemophiliacs, but in contrast to hemophilia A mice which rarely bleed under standard breed conditions. Infusion of human factor VIII was effective in stopping bleeding and reducing the bleeding frequency of a hemophilia A piglet but was blocked by the inhibitor against human factor VIII. These data suggest that the hemophilia A pig is a severe hemophilia A animal model for studying not only hemophilia A gene therapy but also the next generation recombinant coagulation factors, such as recombinant factor VIII variants with a slower clearance rate.     

血友病A的基因治疗研究进展

血友病A是由于编码凝血因子Ⅷ (简称FⅧ )的基因先天性异常而导致的机体出血紊乱性遗传病 ,基因治疗是彻底治愈血友病A的一种最为理想的治疗措施 .就FⅧ基因及其蛋白质分子的结构与性质、基因治疗载体构建、靶细胞、动物模型及其临床应用作一简要综述 .     

Reproduction in Hemophilia

Patterns of marriage and parenthood were studied in the families of 250 patients with severe hemophilia. The incidence of marriage among adult hemophiliacs was 82.5 percent that of age-matched males of the general United States population, as of 1968. Married hemophiliacs 30 years old or older had an average of 2.1 children each, as of 1971. In the periods 1950-1954 and 1960-1964, the numbers of children sired by hemophiliacs were 25 and 38 percent, respectively, of the numbers expected of age-matched men of the general United States population. This indicates a lesser ability or willingness to have children. The number of additional births to women who were already mothers of hemophiliacs was compared with that expected for women of the general population of the United States, matched for age and parity. In the years 1940 through 1954, the birthrates for the two groups were similar. However, in the years 1955-1968, the birthrate among carriers declined more rapidly than that in the general population. The improved medical treatment of hemophilia has apparently not resulted in a greater willingness of affected persons to transmit the defective gene.