Citation: | Xiangyu Yang, Yafei Mao, Xuan-Kai Wang, Dong-Ni Ma, Zhen Xu, Neng Gong, Barbara Henning, Xu Zhang, Guang He, Yong-Yong Shi, Evan E. Eichler, Zhi-Qiang Li, Eiki Takahashi, Wei-Dong Li. Population genetics of marmosets in Asian primate research centers and loci associated with epileptic risk revealed by whole-genome sequencing. Zoological Research, 2023, 44(5): 837-847. doi: 10.24272/j.issn.2095-8137.2022.514 |
[1] |
Battaglia A, Guerrini R. 2005. Chromosomal disorders associated with epilepsy. Epileptic Disorders, 7(3): 181−192.
|
[2] |
Benirschke K, Anderson JM, Brownhill LE. 1962. Marrow chimerism in marmosets.
|
[3] |
Breton VL, Aquilino MS, Repudi S, et al. 2021. Altered neocortical oscillations and cellular excitability in an in vitro Wwox knockout mouse model of epileptic encephalopathy.
|
[4] |
Carlson J, Li JZ, Zöllner S. 2018. Helmsman: fast and efficient mutation signature analysis for massive sequencing datasets.
|
[5] |
Chen JC, Lee G, Fanous AH, et al. 2011. Two non-synonymous markers in PTPN21, identified by genome-wide association study data-mining and replication, are associated with schizophrenia. Schizophrenia Research, 131(1–3): 43–51.
|
[6] |
Chen XY, Schulz-Trieglaff O, Shaw R, et al. 2016. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.
|
[7] |
Coe BP, Witherspoon K, Rosenfeld JA, et al. 2014. Refining analyses of copy number variation identifies specific genes associated with developmental delay.
|
[8] |
Cooper GM, Coe BP, Girirajan S, et al. 2011. A copy number variation morbidity map of developmental delay.
|
[9] |
Ekenstedt KJ, Patterson EE, Mickelson JR. 2012. Canine epilepsy genetics. Mammalian Genome, 23(1–2): 28–39.
|
[10] |
Ellis CA, Petrovski S, Berkovic SF. 2020. Epilepsy genetics: clinical impacts and biological insights.
|
[11] |
Gardiner RM. 2000. Impact of our understanding of the genetic aetiology of epilepsy.
|
[12] |
Grzybowska EA. 2012. Human intronless genes: functional groups, associated diseases, evolution, and mRNA processing in absence of splicing.
|
[13] |
Hardies K, Weckhuysen S, De Jonghe P, et al. 2016. Lessons learned from gene identification studies in Mendelian epilepsy disorders.
|
[14] |
Helbig I, Mefford HC, Sharp AJ, et al. 2009. 15q13.3 microdeletions increase risk of idiopathic generalized epilepsy.
|
[15] |
Homman-Ludiye J, Bourne JA. 2020. The marmoset: the next frontier in understanding the development of the human brain. ILAR Journal, 61(2–3): 248–259.
|
[16] |
Hsu CY, Lee KT, Sun TY, et al. 2021. WWOX and its binding proteins in neurodegeneration.
|
[17] |
Iacomino M, Baldassari S, Tochigi Y, et al. 2020. Loss of Wwox perturbs neuronal migration and impairs early cortical development.
|
[18] |
Johannsen J, Kortüm F, Rosenberger G, et al. 2018. A novel missense variant in the SDR domain of the WWOX gene leads to complete loss of WWOX protein with early-onset epileptic encephalopathy and severe developmental delay.
|
[19] |
Kishi N, Sato K, Sasaki E, et al. 2014. Common marmoset as a new model animal for neuroscience research and genome editing technology. Development, Growth & Differentiation, 56(1): 53−62.
|
[20] |
Kos MZ, Carless MA, Blondell L, et al. 2021. Whole genome sequence data from captive baboons implicate RBFOX1 in epileptic seizure risk.
|
[21] |
Kulyté A, Aman A, Strawbridge RJ, et al. 2022. Genome-wide association study identifies genetic loci associated with fat cell number and overlap with genetic risk loci for type 2 diabetes.
|
[22] |
Leu C, Stevelink R, Smith AW, et al. 2019. Polygenic burden in focal and generalized epilepsies.
|
[23] |
Li H. 2011. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data.
|
[24] |
Li H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv,doi: arXiv:1303.3997.
|
[25] |
Li H, Handsaker B, Wysoker A, et al. 2009. The sequence alignment/map format and SAMtools.
|
[26] |
Li MY, Boehnke M, Abecasis GR. 2005. Joint modeling of linkage and association: identifying SNPs responsible for a linkage signal.
|
[27] |
Li MY, Boehnke M, Abecasis GR. 2006. Efficient study designs for test of genetic association using sibship data and unrelated cases and controls.
|
[28] |
Liu ZP, Xiang YQ, Sun GH. 2013. The KCTD family of proteins: structure, function, disease relevance. Cell & Bioscience, 3(1): 45.
|
[29] |
Malukiewicz J, Boere V, De Oliveira MAB, et al. 2020. An introduction to the Callithrix genus and overview of recent advances in marmoset research. ILAR Journal, 61(2–3): 110–138.
|
[30] |
Manichaikul A, Mychaleckyj JC, Rich SS, et al. 2010. Robust relationship inference in genome-wide association studies.
|
[31] |
Mao YF, Economo EP, Satoh N. 2018. The roles of introgression and climate change in the rise to dominance of Acropora corals.
|
[32] |
Marshall GF, Gonzalez-Sulser A, Abbott CM. 2021. Modelling epilepsy in the mouse: challenges and solutions. Disease Models & Mechanisms, 14(3): dmm047449.
|
[33] |
Martin M, Patterson M, Garg S, et al. 2016. WhatsHap: fast and accurate read-based phasing. BioRxiv, doi: https://doi.org/10.1101/085050.
|
[34] |
McKenna A, Hanna M, Banks E, et al. 2010. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
|
[35] |
Moreau C, Rébillard RM, Wolking S, et al. 2020. Polygenic risk scores of several subtypes of epilepsies in a founder population.
|
[36] |
Mullen SA, Berkovic SF, the ILAE Genetics Commission. 2018. Genetic generalized epilepsies.
|
[37] |
National Academies of Sciences, Engineering, and Medicine. 2019. Care, use, and welfare of marmosets as animal models for gene editing-based biomedical research. In: Proceedings of a Workshop. Washington: The National Academies Press.
|
[38] |
Nishijima K, Saitoh R, Tanaka S, et al. 2012. Life span of common marmoset (Callithrix jacchus) at CLEA Japan breeding colony.
|
[39] |
Okano H, Mitra P. 2015. Brain-mapping projects using the common marmoset.
|
[40] |
Okano H, Sasaki E, Yamamori T, et al. 2016. Brain/MINDS: a Japanese national brain project for marmoset neuroscience.
|
[41] |
Patterson M, Marschall T, Pisanti N, et al. 2015. WhatsHap: weighted haplotype assembly for future-generation sequencing reads.
|
[42] |
Pedersen B. 2018. Smoove: structural variant calling and genotyping with existing tools, but, smoothly.https://github.com/brentp/smoove.
|
[43] |
Plani-Lam JHC, Chow TC, Siu KL, et al. 2015. PTPN21 exerts pro-neuronal survival and neuritic elongation via ErbB4/NRG3 signaling. The International Journal of Biochemistry & Cell Biology, 61: 53−62.
|
[44] |
Poo MM, Du JL, Ip NY, et al. 2016. China brain project: basic neuroscience, brain diseases, and brain-inspired computing.
|
[45] |
Purcell S, Neale B, Todd-Brown K, et al. 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses.
|
[46] |
Repudi S, Steinberg DJ, Elazar N, et al. 2021. Neuronal deletion of Wwox, associated with WOREE syndrome, causes epilepsy and myelin defects.
|
[47] |
Robinson R, Gardiner M. 2004. Molecular basis of Mendelian idiopathic epilepsies.
|
[48] |
Ross CN, French JA, Ortí G. 2007. Germ-line chimerism and paternal care in marmosets (Callithrix kuhlii). Proceedings of the National Academy of Sciences of the United States of America, 104(15): 6278−6282.
|
[49] |
Sato K, Kuroki Y, Kumita W, et al. 2015. Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis.
|
[50] |
Scharfman HE. 2007. The neurobiology of epilepsy.
|
[51] |
Shimogori T, Abe A, Go Y, et al. 2018. Digital gene atlas of neonate common marmoset brain.
|
[52] |
Shorvon SD. 2011. The etiologic classification of epilepsy.
|
[53] |
Stewart I. 2010. Environmental risk factors for temporal lobe epilepsy–Is prenatal exposure to the marine algal neurotoxin domoic acid a potentially preventable cause?.
|
[54] |
Sweeney CG, Curran E, Westmoreland SV, et al. 2012. Quantitative molecular assessment of chimerism across tissues in marmosets and tamarins.
|
[55] |
Teng XC, Aouacheria A, Lionnard L, et al. 2019. KCTD: a new gene family involved in neurodevelopmental and neuropsychiatric disorders. CNS Neuroscience & Therapeutics, 25(7): 887−902.
|
[56] |
The Marmoset Genome Sequencing and Analysis Consortium. 2014. The common marmoset genome provides insight into primate biology and evolution.
|
[57] |
Thijs RD, Surges R, O'Brien TJ, et al. 2019. Epilepsy in adults.
|
[58] |
Thomas RH, Berkovic SF. 2014. The hidden genetics of epilepsy—a clinically important new paradigm.
|
[59] |
Usui D, Shimada S, Shimojima K, et al. 2013. Interstitial duplication of 2q32.1–q33.3 in a patient with epilepsy, developmental delay, and autistic behavior.
|
[60] |
Warren WC, Harris RA, Haukness M, et al. 2020. Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility.
|
[61] |
Wielaender F, Sarviaho R, James F, et al. 2017. Generalized myoclonic epilepsy with photosensitivity in juvenile dogs caused by a defective DIRAS family GTPase 1. Proceedings of the National Academy of Sciences of the United States of America, 114(10): 2669−2674.
|
[62] |
Yang CT, Zhou Y, Marcus S, et al. 2021. Evolutionary and biomedical insights from a marmoset diploid genome assembly.
|
[63] |
Yang XY, Chen ZT, Wang ZY, et al. 2022. A natural marmoset model of genetic generalized epilepsy.
|
[64] |
Ye J, Coulouris G, Zaretskaya I, et al. 2012. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction.
|
[65] |
Youlatos D. 2009. The smallest anthropoids. Journal of Long-Term Effects of Medical Implants, 18(2): 175−179.
|
![]() |
![]() |