A new mouse SNP genotyping assay for speed congenics: combining flexibility, affordability, and power.
A new mouse SNP genotyping assay for speed congenics: combining flexibility, affordability, and power.
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DOI：
10.1186/s12864-021-07698-9
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发表时间：
2021-05-24
期刊：
影响因子：
4.4
通讯作者：
Luckhart S
中科院分区：
文献类型：
--
作者：
Andrews KR;Hunter SS;Torrevillas BK;Céspedes N;Garrison SM;Strickland J;Wagers D;Hansten G;New DD;Fagnan MW;Luckhart S
快速基因是构建基因小鼠以研究基因功能的重要工具，但目前用于快速基因的SNP基因分型方法价格昂贵。这些方法通常依赖于芯片或阵列技术，并且必须为每个回交菌株组合开发不同的检测方法。“下一代”高通量DNA测序技术具有降低成本、增加灵活性和快速同源能力的潜力，但迄今尚未用于此目的。我们利用高通量测序技术的优势，开发了一种具有成本效益的高密度SNP基因分型分析方法，可用于许多回交菌株的组合。该分析调查了1640个已知在bb100个小鼠品系中具有多态性的全基因组snp，预计每对品系之间的平均诊断snp为549±136个SD。结果表明，BALB/c与C57BL/6J的回交诊断snp密度较高（807-819个SNPs），与C57BL/6N和C57BL/6J的回交诊断snp密度较高（123-139个SNPs）。此外，该分析可以很容易地进行修改，以包括回交其他密切相关的子菌株的附加诊断snp。我们还开发了一个生物信息学管道，用于SNP基因分型和计算每个样本与回交受体菌株匹配的等位基因百分比；这些信息可以用来指导下一次回交的个体选择，并评估个体是否具有同源性。我们通过BALB/c-IL4/IL13与C57BL/6J的回交实验证明了该方法和生物信息管道的有效性；回交6代后，后代的遗传率高达99.8%。这里开发的SNP基因分型分析和生物信息学管道提供了一个有价值的工具，可以提高许多依赖于快速同源的研究的能力和降低成本。该分析是高度灵活的，可用于通常用于速度同源菌株的组合。该分析也可用于其他技术，包括QTL定位、标准F2杂交、祖先分析和法医学。在线版本包含补充材料，可在10.1186/s12864-021-07698-9获得。
Speed congenics is an important tool for creating congenic mice to investigate gene functions, but current SNP genotyping methods for speed congenics are expensive. These methods usually rely on chip or array technologies, and a different assay must be developed for each backcross strain combination. “Next generation” high throughput DNA sequencing technologies have the potential to decrease cost and increase flexibility and power of speed congenics, but thus far have not been utilized for this purpose. We took advantage of the power of high throughput sequencing technologies to develop a cost-effective, high-density SNP genotyping assay that can be used across many combinations of backcross strains. The assay surveys 1640 genome-wide SNPs known to be polymorphic across > 100 mouse strains, with an expected average of 549 ± 136 SD diagnostic SNPs between each pair of strains. We demonstrated that the assay has a high density of diagnostic SNPs for backcrossing the BALB/c strain into the C57BL/6J strain (807–819 SNPs), and a sufficient density of diagnostic SNPs for backcrossing the closely related substrains C57BL/6N and C57BL/6J (123–139 SNPs). Furthermore, the assay can easily be modified to include additional diagnostic SNPs for backcrossing other closely related substrains. We also developed a bioinformatic pipeline for SNP genotyping and calculating the percentage of alleles that match the backcross recipient strain for each sample; this information can be used to guide the selection of individuals for the next backcross, and to assess whether individuals have become congenic. We demonstrated the effectiveness of the assay and bioinformatic pipeline with a backcross experiment of BALB/c-IL4/IL13 into C57BL/6J; after six generations of backcrosses, offspring were up to 99.8% congenic. The SNP genotyping assay and bioinformatic pipeline developed here present a valuable tool for increasing the power and decreasing the cost of many studies that depend on speed congenics. The assay is highly flexible and can be used for combinations of strains that are commonly used for speed congenics. The assay could also be used for other techniques including QTL mapping, standard F2 crosses, ancestry analysis, and forensics. The online version contains supplementary material available at 10.1186/s12864-021-07698-9.
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DOI：
10.1038/mtna.2015.37
发表时间：
2015-11-17
期刊：
Molecular therapy. Nucleic acids
影响因子：
--
作者：
Zhang XH;Tee LY;Wang XG;Huang QS;Yang SH
通讯作者：
Yang SH
影响因子：
2.5
作者：
Armstrong, NJ;Brodnicki, TC;Speed, TP
通讯作者：
Speed, TP
影响因子：
4.3
作者：
Rodriguez-Gil, Jorge L.;Watkins-Chow, Dawn E.;Pavan, William J.
通讯作者：
Pavan, William J.
影响因子：
4.4
作者：
Farkas, C.;Fuentes-Villalobos, F.;Pincheira, R.
通讯作者：
Pincheira, R.
影响因子：
3.3
作者：
Sigmon JS;Blanchard MW;Baric RS;Bell TA;Brennan J;Brockmann GA;Burks AW;Calabrese JM;Caron KM;Cheney RE;Ciavatta D;Conlon F;Darr DB;Faber J;Franklin C;Gershon TR;Gralinski L;Gu B;Gaines CH;Hagan RS;Heimsath EG;Heise MT;Hock P;Ideraabdullah F;Jennette JC;Kafri T;Kashfeen A;Kulis M;Kumar V;Linnertz C;Livraghi-Butrico A;Lloyd KCK;Lutz C;Lynch RM;Magnuson T;Matsushima GK;McMullan R;Miller DR;Mohlke KL;Moy SS;Murphy CEY;Najarian M;O'Brien L;Palmer AA;Philpot BD;Randell SH;Reinholdt L;Ren Y;Rockwood S;Rogala AR;Saraswatula A;Sassetti CM;Schisler JC;Schoenrock SA;Shaw GD;Shorter JR;Smith CM;St Pierre CL;Tarantino LM;Threadgill DW;Valdar W;Vilen BJ;Wardwell K;Whitmire JK;Williams L;Zylka MJ;Ferris MT;McMillan L;Manuel de Villena FP
通讯作者：
Manuel de Villena FP