Whole-genome sequence of Macaca fascicularis: liver tissue

BMC Genomic Data - Tập 24 - Trang 1-3 - 2023
Eun-Hye Seo1, Jeong-Hwan Kim2, Da-Hee Kim3, Jung-Hwa Oh4, Seon-Young Kim1
1Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
2Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
3Jeonbuk Branch, Korea Institute of Toxicology, Jeonbuk, Republic of Korea
4Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, Republic of Korea

Tóm tắt

Thrombocytopenia is a condition that causes a low amount of blood platelets. Platelets are blood cells that play an essential role in blood coagulation. Therefore, thrombocytopenia can put the patient at risk for mild to severe bleeding. Thrombocytopenia is caused by a decrease in platelet production in the bone marrow or by a drug or immune system problem when production is normal. In particular, in some ASO-induced thrombocytopenia, the mechanism is not clear. Therefore, whole genome sequencing (WGS) was performed to discover genetic differences that affect thrombocytopenia and individual susceptibility to drugs between normal and reduced platelet monkeys despite administering the same ASO. Three antisense oligonucleotide (ASO) substances were injected into the subcutaneous tissue of monkeys for 12 weeks in two experiments. The monkeys were classified into three groups: monkeys with thrombocytopenia, monkeys without thrombocytopenia, and control monkeys not treated with ASO substances. Whole genome sequencing data was generated using liver tissues of monkeys. These data will be useful for identifying genetic differences that affect thrombocytopenia and drug sensitivity.

Tài liệu tham khảo

Gauer RL, Braun MM. Thrombocytopenia. Am Fam Physician. 2012;85(6):612–22. Smock KJ, Perkins SL. Thrombocytopenia: an update. Int J Lab Hematol. 2014;36(3):269–78. Watts JK, Corey DR. Silencing disease genes in the laboratory and the clinic. J Pathol. 2012;226(2):365–79. Roberts TC, Langer R, Wood MJA. Advances in oligonucleotide drug delivery. Nat Rev Drug Discov. 2020;19(10):673–94. Scoles DR, Minikel EV, Pulst SM. Antisense oligonucleotides: a primer. Neurol Genet. 2019;5(2):e323. Lim KR, Maruyama R, Yokota T. Eteplirsen in the treatment of Duchenne muscular dystrophy. Drug Des Devel Ther. 2017;11:533–45. Benson MD, Waddington-Cruz M, Berk JL, Polydefkis M, Dyck PJ, Wang AK, Plante-Bordeneuve V, Barroso FA, Merlini G, Obici L, et al. Inotersen treatment for patients with hereditary transthyretin amyloidosis. N Engl J Med. 2018;379(1):22–31. Finkel RS, Mercuri E, Darras BT, Connolly AM, Kuntz NL, Kirschner J, Chiriboga CA, Saito K, Servais L, Tizzano E, et al. Nusinersen versus sham control in infantile-onset spinal muscular atrophy. N Engl J Med. 2017;377(18):1723–32. Miller T, Cudkowicz M, Shaw PJ, Andersen PM, Atassi N, Bucelli RC, Genge A, Glass J, Ladha S, Ludolph AL, et al. Phase 1–2 trial of antisense oligonucleotide Tofersen for SOD1 ALS. N Engl J Med. 2020;383(2):109–19. Clemens PR, Rao VK, Connolly AM, Harper AD, Mah JK, Smith EC, McDonald CM, Zaidman CM, Morgenroth LP, Osaki H, et al. Safety, tolerability, and efficacy of viltolarsen in boys with duchenne muscular dystrophy amenable to exon 53 skipping: a phase 2 randomized clinical trial. JAMA Neurol. 2020;77(8):982–91. De Velasco MA, Kura Y, Sakai K, Hatanaka Y, Davies BR, Campbell H, et al. Targeting castration-resistant prostate cancer with androgen receptor antisense oligonucleotide therapy. JCI Insight. 2019;4(17):e122688. Tabrizi SJ, Leavitt BR, Landwehrmeyer GB, Wild EJ, Saft C, Barker RA, Blair NF, Craufurd D, Priller J, Rickards H, et al. Targeting huntingtin expression in patients with huntington’s disease. N Engl J Med. 2019;380(24):2307–16. Seo, EH. 1st analysis PLT counts. figshare. Dataset. 2022. https://doi.org/10.6084/m9.figshare.19736242. Seo, EH. 2nd analysis of PLT counts. figshare. Dataset. 2022. https://doi.org/10.6084/m9.figshare.19738171. Seo, EH. Quality and quantity of the sequencing data. figshare. Dataset. 2022. https://doi.org/10.6084/m9.figshare.19738336. 1st analysis: Korea Nucleotide Archive. 2022. https://kobic.re.kr/kona. 2nd analysis: Korea Nucleotide Archive. 2022. https://kobic.re.kr/kona. NCBI Sequence Read Archive. Whole genome seq of Macaca fascicularis: liver tissue. 2022. https://identifiers.org/ncbi/insdc.sra:SRP409432. Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at arXiv. 2013. https://arxiv.org/abs/1303.3997. Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, Jordan T, Shakir K, Roazen D, Thibault J, et al. From FastQ data to high confidence variant calls: the Genome analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics. 2013;43:11 10 11-11 10 33. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008;456(7218):53–9.