Seong Gyu Kwon1,2, Geon Hue Bae1,2, June Hyug Choi1, Nanda Maya Mali1,3, Mee Sook Jun1,3, Dong Sun Kim1,2, Man-Hoon Han3,4, Seongyeol Park5, Young Seok Ju5, Seock Hwan Choi6,7, Ji Won Oh8,9,10,11. 1. Department of Anatomy, School of Medicine, Kyungpook National University, Daegu, Republic of Korea. 2. BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea. 3. Biomedical Research Institute, Kyungpook National University Hospital, Daegu, Republic of Korea. 4. Department of Pathology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea. 5. Graduate School of Medical Science and Engineering (GSMSE), Korea Advanced Institute of Science and Technology (KAIST) and GENOME INSIGHT Inc, Daejeon, Republic of Korea. 6. Biomedical Research Institute, Kyungpook National University Hospital, Daegu, Republic of Korea. skhwan.script@gmail.com. 7. Department of Urology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea. skhwan.script@gmail.com. 8. Department of Anatomy, School of Medicine, Kyungpook National University, Daegu, Republic of Korea. G1@yuhs.ac. 9. BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea. G1@yuhs.ac. 10. Biomedical Research Institute, Kyungpook National University Hospital, Daegu, Republic of Korea. G1@yuhs.ac. 11. Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea. G1@yuhs.ac.
Abstract
BACKGROUND: In humans, after fertilization, the zygote divides into two 2n diploid daughter blastomeres. During this division, DNA is replicated, and the remaining mutually exclusive genetic mutations in the genome of each cell are called post-zygotic variants. Using these somatic mutations, developmental lineages can be reconstructed. How these two blastomeres are contributing to the entire body is not yet identified. This study aims to evaluate the cellular contribution of two blastomeres of 2-cell embryos to the entire body in humans using post-zygotic variants based on whole genome sequencing. METHODS: Tissues from different anatomical areas were obtained from five donated cadavers for use in single-cell clonal expansion and bulk target sequencing. After conducting whole genome sequencing, computational analysis was applied to find the early embryonic mutations of each clone. We developed our in-house bioinformatics pipeline, and filtered variants using strict criteria, composed of mapping quality, base quality scores, depth, soft-clipped reads, and manual inspection, resulting in the construction of embryological phylogenetic cellular trees. RESULTS: Using our in-house pipeline for variant filtering, we could extract accurate true positive variants, and construct the embryological phylogenetic trees for each cadaver. We found that two daughter blastomeres, L1 and L2 (lineage 1 and 2, respectively), derived from the zygote, distribute unequally to the whole body at the clonal level. From bulk target sequencing data, we validated asymmetric contribution by means of the variant allele frequency of L1 and L2. The asymmetric contribution of L1 and L2 varied from person to person. CONCLUSION: We confirmed that there is asymmetric contribution of two daughter blastomeres from the first division of the zygote across the whole human body.
BACKGROUND: In humans, after fertilization, the zygote divides into two 2n diploid daughter blastomeres. During this division, DNA is replicated, and the remaining mutually exclusive genetic mutations in the genome of each cell are called post-zygotic variants. Using these somatic mutations, developmental lineages can be reconstructed. How these two blastomeres are contributing to the entire body is not yet identified. This study aims to evaluate the cellular contribution of two blastomeres of 2-cell embryos to the entire body in humans using post-zygotic variants based on whole genome sequencing. METHODS: Tissues from different anatomical areas were obtained from five donated cadavers for use in single-cell clonal expansion and bulk target sequencing. After conducting whole genome sequencing, computational analysis was applied to find the early embryonic mutations of each clone. We developed our in-house bioinformatics pipeline, and filtered variants using strict criteria, composed of mapping quality, base quality scores, depth, soft-clipped reads, and manual inspection, resulting in the construction of embryological phylogenetic cellular trees. RESULTS: Using our in-house pipeline for variant filtering, we could extract accurate true positive variants, and construct the embryological phylogenetic trees for each cadaver. We found that two daughter blastomeres, L1 and L2 (lineage 1 and 2, respectively), derived from the zygote, distribute unequally to the whole body at the clonal level. From bulk target sequencing data, we validated asymmetric contribution by means of the variant allele frequency of L1 and L2. The asymmetric contribution of L1 and L2 varied from person to person. CONCLUSION: We confirmed that there is asymmetric contribution of two daughter blastomeres from the first division of the zygote across the whole human body.
Authors: Aaron McKenna; Matthew Hanna; Eric Banks; Andrey Sivachenko; Kristian Cibulskis; Andrew Kernytsky; Kiran Garimella; David Altshuler; Stacey Gabriel; Mark Daly; Mark A DePristo Journal: Genome Res Date: 2010-07-19 Impact factor: 9.043
Authors: Claudia Gerri; Sergio Menchero; Shantha K Mahadevaiah; James M A Turner; Kathy K Niakan Journal: Annu Rev Cell Dev Biol Date: 2020-10-06 Impact factor: 13.827