323
Natural Genetic Variation and Disease
fetal alcohol syndrome. Biochem. Cell Biol. 96, 148–160.
doi:10.1139/bcb-2017-0132
Shabtai, Y., Jubran, H., Nassar, T., Hirschberg, J., Fainsod, A.,
2016. Kinetic characterization and regulation of the human
retinaldehyde dehydrogenase 2 enzyme during production
of retinoic acid. Biochem. J. 473, 1423–1431. doi:10.1042/
BCJ20160101
Shah, A.M., Krohn, P., Baxi, A.B., Tavares, A.L.P., Sullivan,
C.H., Chillakuru, Y.R., Majumdar, H.D., Neilson, K.M.,
Moody, S.A., 2020. Six1 proteins with human branchiooto-renal mutations differentially affect cranial gene expression and otic development. Dis. Model. Mech. doi:10.1242/
dmm.043489
Sharma, D., Shastri, S., Farahbakhsh, N., Sharma, P., 2016.
Intrauterine growth restriction—part 1. J. Matern. Fetal
Neonatal Med. 29, 3977–3987. doi:10.3109/14767058.201
6.1152249
Sharma, D., Sharma, P., Shastri, S., 2017. Genetic, metabolic and
endocrine aspect of intrauterine growth restriction: an update.
J. Matern. Fetal Neonatal Med. 30, 2263–2275. doi:10.1080
/14767058.2016.1245285
Shinya, M., Sakai, N., 2011. Generation of highly homogeneous strains of zebrafsh through full sib-pair mating. G3
(Bethesda) 1, 377–386. doi:10.1534/g3.111.000851
Shukrun, N., Shabtai, Y., Pillemer, G., Fainsod, A., 2019. Retinoic
acid signaling reduction recapitulates the effects of alcohol
on embryo size. Genesis 57, e23284. doi:10.1002/dvg.23284
Simon, M.M., Greenaway, S., White, J.K., Fuchs, H., Gailus-Durner,
V., Wells, S., Sorg, T., Wong, K., Bedu, E., Cartwright, E.J.,
Dacquin, R., Djebali, S., Estabel, J., Graw, J., Ingham, N.J.,
Jackson, I.J., Lengeling, A., Mandillo, S., Marvel, J., Meziane,
H., Brown, S.D.M., 2013. A comparative phenotypic and
genomic analysis of C57BL/6J and C57BL/6N mouse strains.
Genome Biol. 14, R82. doi:10.1186/gb-2013-14-7-r82
Simpson, E.M., Linder, C.C., Sargent, E.E., Davisson, M.T.,
Mobraaten, L.E., Sharp, J.J., 1997. Genetic variation among
129 substrains and its importance for targeted mutagenesis in
mice. Nat. Genet. 16, 19–27. doi:10.1038/ng0597-19
Singh, A., Allen, D., Fracassi, A., Tumurbaatar, B., Natarajan, C.,
Scaduto, P., Woltjer, R., Kayed, R., Limon, A., Krishnan, B.,
Taglialatela, G., 2020. Functional integrity of synapses in
the central nervous system of cognitively intact individuals
with high Alzheimer’s disease neuropathology is associated
with absence of synaptic tau oligomers. J Alzheimers Dis.
doi:10.3233/JAD-200716
Sommardahl, C., Cottrell, M., Wilkinson, J.E., Woychik, R.P.,
Johnson, D.K., 2001. Phenotypic variations of orpk mutation
and chromosomal localization of modif ers inf uencing kidney phenotype. Physiol. Genomics 7, 127–134. doi:10.1152/
physiolgenomics.00089.2001
Spielmann, M., Lupiáñez, D.G., Mundlos, S., 2018. Structural
variation in the 3D genome. Nat. Rev. Genet. 19, 453–467.
doi:10.1038/s41576-018-0007-0
Spivakov, M., Auer, T.O., Peravali, R., Dunham, I., Dolle, D.,
Fujiyama, A., Toyoda, A., Aizu, T., Minakuchi, Y., Loosli, F.,
Naruse, K., Birney, E., Wittbrodt, J., 2014. Genomic and phenotypic characterization of a wild medaka population: Towards
the establishment of an isogenic population genetic resource in
f sh. G3 (Bethesda) 4, 433–445. doi:10.1534/g3.113.008722
Stenson, P.D., Mort, M., Ball, E.V., Evans, K., Hayden, M.,
Heywood, S., Hussain, M., Phillips, A.D., Cooper, D.N.,
2017. The human gene mutation database: Towards a comprehensive repository of inherited mutation data for medical
research, genetic diagnosis and next-generation sequencing
studies. Hum. Genet. 136, 665–677. doi:10.1007/s00439017-1779-6
Stevens, L.C., Hummel, K.P., 1957. A description of spontaneous
congenital testicular teratomas in strain 129 mice. J Natl
Cancer Inst 18, 719–747.
Streisinger, G., Walker, C., Dower, N., Knauber, D., Singer, F.,
1981. Production of clones of homozygous diploid zebra
f sh (Brachydanio rerio). Nature 291, 293–296. doi:10.
1038/291293a0
Sun, J., Wiklund, F., Hsu, F.-C., Bälter, K., Zheng, S.L., Johansson,
J.-E., Chang, B., Liu, W., Li, T., Turner, A.R., Li, L., Li, G.,
Adami, H.-O., Isaacs, W.B., Xu, J., Grönberg, H., 2006.
Interactions of sequence variants in interleukin-1 receptor-associated kinase4 and the toll-like receptor 6–1–10 gene cluster
increase prostate cancer risk. Cancer Epidemiol. Biomarkers
Prev. 15, 480–485. doi:10.1158/1055–9965.EPI-05-0645
Suurväli, J., Whiteley, A.R., Zheng, Y., Gharbi, K., Leptin, M.,
Wiehe, T., 2020. The laboratory domestication of zebraf sh:
From diverse populations to inbred substrains. Mol. Biol.
Evol. 37, 1056–1069. doi:10.1093/molbev/msz289
Taketo, M., Schroeder, A.C., Mobraaten, L.E., Gunning, K.B.,
Hanten, G., Fox, R.R., Roderick, T.H., Stewart, C.L., Lilly,
F., Hansen, C.T., 1991. FVB/N: An inbred mouse strain preferable for transgenic analyses. Proc Natl Acad Sci USA 88,
2065–2069. doi:10.1073/pnas.88.6.2065
Tandon, P., Conlon, F., Furlow, J.D., Horb, M.E., 2017. Expanding
the genetic toolkit in Xenopus: Approaches and opportunities for human disease modeling. Dev. Biol. 426, 325–335.
doi:10.1016/j.ydbio.2016.04.009
Threadgill, D.W., Dlugosz, A.A., Hansen, L.A., Tennenbaum,
T., Lichti, U., Yee, D., LaMantia, C., Mourton, T., Herrup,
K., Harris, R.C., 1995. Targeted disruption of mouse EGF
receptor: Effect of genetic background on mutant phenotype.
Science 269, 230–234. doi:10.1126/science.7618084
Threadgill, D.W., Miller, D.R., Churchill, G.A., de Villena, F.P.-M.,
2011. The collaborative cross: A recombinant inbred mouse
population for the systems genetic era. ILAR J. 52, 24–31.
doi:10.1093/ilar.52.1.24
Threadgill, D.W., Yee, D., Matin, A., Nadeau, J.H., Magnuson,
T., 1997. Genealogy of the 129 inbred strains: 129/SvJ is
a contaminated inbred strain. Mamm. Genome 8, 390–393.
doi:10.1007/s003359900453
Tomlinson, M.L., Hendry, A.E., Wheeler, G.N., 2012. Chemical
genetics and drug discovery in Xenopus. Methods Mol. Biol.
917, 155–166. doi:10.1007/978-1-61779-992-1_9
Török, H.P., Bellon, V., Konrad, A., Lacher, M., Tonenchi, L.,
Siebeck, M., Brand, S., De Toni, E.N., 2017. Functional
toll-like receptor (TLR)2 polymorphisms in the susceptibility to inf ammatory bowel disease. PLoS One 12, e0175180.
doi:10.1371/journal.pone.0175180
Tour, E., Pillemer, G., Gruenbaum, Y., Fainsod, A., 2001. The
two Xenopus Gbx2 genes exhibit similar, but not identical
expression patterns and can affect head formation. FEBS
Lett. 507, 205–209.
Tuttle, A.H., Philip, V.M., Chesler, E.J., Mogil, J.S., 2018.
Comparing phenotypic variation between inbred and outbred mice. Nat. Methods 15, 994–996. doi:10.1038/s41592018-0224-7
Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton,
G.G., Smith, H.O., Yandell, M., Evans, C.A., Holt, R.A.,
Gocayne, J.D., Amanatides, P., Ballew, R.M., Huson, D.H.,
Wortman, J.R., Zhang, Q., Kodira, C.D., Zheng, X.H., Chen, L.,
Skupski, M., et al., 2001. The sequence of the human genome.
Science 291, 1304–1351. doi:10.1126/science.1058040
Natural Genetic Variation and Disease
fetal alcohol syndrome. Biochem. Cell Biol. 96, 148–160.
doi:10.1139/bcb-2017-0132
Shabtai, Y., Jubran, H., Nassar, T., Hirschberg, J., Fainsod, A.,
2016. Kinetic characterization and regulation of the human
retinaldehyde dehydrogenase 2 enzyme during production
of retinoic acid. Biochem. J. 473, 1423–1431. doi:10.1042/
BCJ20160101
Shah, A.M., Krohn, P., Baxi, A.B., Tavares, A.L.P., Sullivan,
C.H., Chillakuru, Y.R., Majumdar, H.D., Neilson, K.M.,
Moody, S.A., 2020. Six1 proteins with human branchiooto-renal mutations differentially affect cranial gene expression and otic development. Dis. Model. Mech. doi:10.1242/
dmm.043489
Sharma, D., Shastri, S., Farahbakhsh, N., Sharma, P., 2016.
Intrauterine growth restriction—part 1. J. Matern. Fetal
Neonatal Med. 29, 3977–3987. doi:10.3109/14767058.201
6.1152249
Sharma, D., Sharma, P., Shastri, S., 2017. Genetic, metabolic and
endocrine aspect of intrauterine growth restriction: an update.
J. Matern. Fetal Neonatal Med. 30, 2263–2275. doi:10.1080
/14767058.2016.1245285
Shinya, M., Sakai, N., 2011. Generation of highly homogeneous strains of zebrafsh through full sib-pair mating. G3
(Bethesda) 1, 377–386. doi:10.1534/g3.111.000851
Shukrun, N., Shabtai, Y., Pillemer, G., Fainsod, A., 2019. Retinoic
acid signaling reduction recapitulates the effects of alcohol
on embryo size. Genesis 57, e23284. doi:10.1002/dvg.23284
Simon, M.M., Greenaway, S., White, J.K., Fuchs, H., Gailus-Durner,
V., Wells, S., Sorg, T., Wong, K., Bedu, E., Cartwright, E.J.,
Dacquin, R., Djebali, S., Estabel, J., Graw, J., Ingham, N.J.,
Jackson, I.J., Lengeling, A., Mandillo, S., Marvel, J., Meziane,
H., Brown, S.D.M., 2013. A comparative phenotypic and
genomic analysis of C57BL/6J and C57BL/6N mouse strains.
Genome Biol. 14, R82. doi:10.1186/gb-2013-14-7-r82
Simpson, E.M., Linder, C.C., Sargent, E.E., Davisson, M.T.,
Mobraaten, L.E., Sharp, J.J., 1997. Genetic variation among
129 substrains and its importance for targeted mutagenesis in
mice. Nat. Genet. 16, 19–27. doi:10.1038/ng0597-19
Singh, A., Allen, D., Fracassi, A., Tumurbaatar, B., Natarajan, C.,
Scaduto, P., Woltjer, R., Kayed, R., Limon, A., Krishnan, B.,
Taglialatela, G., 2020. Functional integrity of synapses in
the central nervous system of cognitively intact individuals
with high Alzheimer’s disease neuropathology is associated
with absence of synaptic tau oligomers. J Alzheimers Dis.
doi:10.3233/JAD-200716
Sommardahl, C., Cottrell, M., Wilkinson, J.E., Woychik, R.P.,
Johnson, D.K., 2001. Phenotypic variations of orpk mutation
and chromosomal localization of modif ers inf uencing kidney phenotype. Physiol. Genomics 7, 127–134. doi:10.1152/
physiolgenomics.00089.2001
Spielmann, M., Lupiáñez, D.G., Mundlos, S., 2018. Structural
variation in the 3D genome. Nat. Rev. Genet. 19, 453–467.
doi:10.1038/s41576-018-0007-0
Spivakov, M., Auer, T.O., Peravali, R., Dunham, I., Dolle, D.,
Fujiyama, A., Toyoda, A., Aizu, T., Minakuchi, Y., Loosli, F.,
Naruse, K., Birney, E., Wittbrodt, J., 2014. Genomic and phenotypic characterization of a wild medaka population: Towards
the establishment of an isogenic population genetic resource in
f sh. G3 (Bethesda) 4, 433–445. doi:10.1534/g3.113.008722
Stenson, P.D., Mort, M., Ball, E.V., Evans, K., Hayden, M.,
Heywood, S., Hussain, M., Phillips, A.D., Cooper, D.N.,
2017. The human gene mutation database: Towards a comprehensive repository of inherited mutation data for medical
research, genetic diagnosis and next-generation sequencing
studies. Hum. Genet. 136, 665–677. doi:10.1007/s00439017-1779-6
Stevens, L.C., Hummel, K.P., 1957. A description of spontaneous
congenital testicular teratomas in strain 129 mice. J Natl
Cancer Inst 18, 719–747.
Streisinger, G., Walker, C., Dower, N., Knauber, D., Singer, F.,
1981. Production of clones of homozygous diploid zebra
f sh (Brachydanio rerio). Nature 291, 293–296. doi:10.
1038/291293a0
Sun, J., Wiklund, F., Hsu, F.-C., Bälter, K., Zheng, S.L., Johansson,
J.-E., Chang, B., Liu, W., Li, T., Turner, A.R., Li, L., Li, G.,
Adami, H.-O., Isaacs, W.B., Xu, J., Grönberg, H., 2006.
Interactions of sequence variants in interleukin-1 receptor-associated kinase4 and the toll-like receptor 6–1–10 gene cluster
increase prostate cancer risk. Cancer Epidemiol. Biomarkers
Prev. 15, 480–485. doi:10.1158/1055–9965.EPI-05-0645
Suurväli, J., Whiteley, A.R., Zheng, Y., Gharbi, K., Leptin, M.,
Wiehe, T., 2020. The laboratory domestication of zebraf sh:
From diverse populations to inbred substrains. Mol. Biol.
Evol. 37, 1056–1069. doi:10.1093/molbev/msz289
Taketo, M., Schroeder, A.C., Mobraaten, L.E., Gunning, K.B.,
Hanten, G., Fox, R.R., Roderick, T.H., Stewart, C.L., Lilly,
F., Hansen, C.T., 1991. FVB/N: An inbred mouse strain preferable for transgenic analyses. Proc Natl Acad Sci USA 88,
2065–2069. doi:10.1073/pnas.88.6.2065
Tandon, P., Conlon, F., Furlow, J.D., Horb, M.E., 2017. Expanding
the genetic toolkit in Xenopus: Approaches and opportunities for human disease modeling. Dev. Biol. 426, 325–335.
doi:10.1016/j.ydbio.2016.04.009
Threadgill, D.W., Dlugosz, A.A., Hansen, L.A., Tennenbaum,
T., Lichti, U., Yee, D., LaMantia, C., Mourton, T., Herrup,
K., Harris, R.C., 1995. Targeted disruption of mouse EGF
receptor: Effect of genetic background on mutant phenotype.
Science 269, 230–234. doi:10.1126/science.7618084
Threadgill, D.W., Miller, D.R., Churchill, G.A., de Villena, F.P.-M.,
2011. The collaborative cross: A recombinant inbred mouse
population for the systems genetic era. ILAR J. 52, 24–31.
doi:10.1093/ilar.52.1.24
Threadgill, D.W., Yee, D., Matin, A., Nadeau, J.H., Magnuson,
T., 1997. Genealogy of the 129 inbred strains: 129/SvJ is
a contaminated inbred strain. Mamm. Genome 8, 390–393.
doi:10.1007/s003359900453
Tomlinson, M.L., Hendry, A.E., Wheeler, G.N., 2012. Chemical
genetics and drug discovery in Xenopus. Methods Mol. Biol.
917, 155–166. doi:10.1007/978-1-61779-992-1_9
Török, H.P., Bellon, V., Konrad, A., Lacher, M., Tonenchi, L.,
Siebeck, M., Brand, S., De Toni, E.N., 2017. Functional
toll-like receptor (TLR)2 polymorphisms in the susceptibility to inf ammatory bowel disease. PLoS One 12, e0175180.
doi:10.1371/journal.pone.0175180
Tour, E., Pillemer, G., Gruenbaum, Y., Fainsod, A., 2001. The
two Xenopus Gbx2 genes exhibit similar, but not identical
expression patterns and can affect head formation. FEBS
Lett. 507, 205–209.
Tuttle, A.H., Philip, V.M., Chesler, E.J., Mogil, J.S., 2018.
Comparing phenotypic variation between inbred and outbred mice. Nat. Methods 15, 994–996. doi:10.1038/s41592018-0224-7
Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton,
G.G., Smith, H.O., Yandell, M., Evans, C.A., Holt, R.A.,
Gocayne, J.D., Amanatides, P., Ballew, R.M., Huson, D.H.,
Wortman, J.R., Zhang, Q., Kodira, C.D., Zheng, X.H., Chen, L.,
Skupski, M., et al., 2001. The sequence of the human genome.
Science 291, 1304–1351. doi:10.1126/science.1058040