# Using AlphaGenome to predict the cooperativity of multiple SNPs? **URL:** \ **Category:** Community\ **Created:** [July 28, 2025, 5:04am UTC](https://www.alphagenomecommunity.com/t/using-alphagenome-to-predict-the-cooperativity-of-multiple-snps/530 "2025-07-28T05:04:28Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![Steve\_S](https://yyz2.discourse-cdn.com/watermelon/user_avatar/www.alphagenomecommunity.com/steve_s/32/417_2.png) [@Steve\_S](https://www.alphagenomecommunity.com/u/Steve_S)\ **Post date:** [July 28, 2025, 5:04am UTC](https://www.alphagenomecommunity.com/t/using-alphagenome-to-predict-the-cooperativity-of-multiple-snps/530/1 "2025-07-28T05:04:28Z")
Hello, Thanks for creating such a powerful tool and making it readily available for the research community. I am an oncologist as well as a research scientist. I have been testing AlphaGenome for the past few days and was impressed by its ability to accurately replicate results for single SNP changes. However, many cancers are associated with haplotypes where multiple SNPs, each tens of thousand BPs apart, jointly alter the DNA expression level/TF binding/splicing. Question: is alphagenome able to predict the cooperativity of multiple SNPs at the same time? Thanks ---
**Author:** ![Jingyu\_Zeng](https://yyz2.discourse-cdn.com/watermelon/user_avatar/www.alphagenomecommunity.com/jingyu_zeng/32/418_2.png) [@Jingyu\_Zeng](https://www.alphagenomecommunity.com/u/Jingyu_Zeng)\ **Post date:** [July 28, 2025, 12:10pm UTC](https://www.alphagenomecommunity.com/t/using-alphagenome-to-predict-the-cooperativity-of-multiple-snps/530/2 "2025-07-28T12:10:36Z")
I have an idea, maybe try it? Since there’s no restriction on variant length, you can try input a variant like this: Chromosome: chr1 (or others) Position: 12345… ref: ACT **G** CGAT **T** ACG (can be longer) alt: ACT **A** CGAT **T** ACG This case showed a two-SNP situation, and you can add more as you wish. There are two problems: 1. You have to find the sequence on the reference genome in this region. Use `samtools faidx hg38.fa chr1:123-456` can do this. 2. The cover region of this variant can be so long, I’m not sure if the result will be weird. And the visualization can be hard too. In my test cases, I tried a 50kb deletion, and still got a result. So it will work, but the result is not known. You can share the result with us! ---
**Author:** ![Steve\_S](https://yyz2.discourse-cdn.com/watermelon/user_avatar/www.alphagenomecommunity.com/steve_s/32/417_2.png) [@Steve\_S](https://www.alphagenomecommunity.com/u/Steve_S)\ **Post date:** [July 28, 2025, 1:58pm UTC](https://www.alphagenomecommunity.com/t/using-alphagenome-to-predict-the-cooperativity-of-multiple-snps/530/3 "2025-07-28T13:58:03Z")
Hi Jingyu, Thanks for replying. I also thought about this but was not sure if the input sequence would be too long. Good to know that 50kb deletion ran just fine. I will give it a try. ---
**Author:** ![Steve\_S](https://yyz2.discourse-cdn.com/watermelon/user_avatar/www.alphagenomecommunity.com/steve_s/32/417_2.png) [@Steve\_S](https://www.alphagenomecommunity.com/u/Steve_S)\ **Post date:** [July 29, 2025, 1:51am UTC](https://www.alphagenomecommunity.com/t/using-alphagenome-to-predict-the-cooperativity-of-multiple-snps/530/4 "2025-07-29T01:51:27Z")
Hi Jingyu, I tried a 7kb sequence with 4 SNPs but it broke AlphaGenome. How was your experience with the large deletion? ---
**Author:** ![Jingyu\_Zeng](https://yyz2.discourse-cdn.com/watermelon/user_avatar/www.alphagenomecommunity.com/jingyu_zeng/32/418_2.png) [@Jingyu\_Zeng](https://www.alphagenomecommunity.com/u/Jingyu_Zeng)\ **Post date:** [July 29, 2025, 5:56am UTC](https://www.alphagenomecommunity.com/t/using-alphagenome-to-predict-the-cooperativity-of-multiple-snps/530/5 "2025-07-29T05:56:25Z")
Can you show me your error? I’m not sure what happened. In my dataset, there are some large indels. They all work well. ---
**Author:** ![Steve\_S](https://yyz2.discourse-cdn.com/watermelon/user_avatar/www.alphagenomecommunity.com/steve_s/32/417_2.png) [@Steve\_S](https://www.alphagenomecommunity.com/u/Steve_S)\ **Post date:** [August 4, 2025, 3:58am UTC](https://www.alphagenomecommunity.com/t/using-alphagenome-to-predict-the-cooperativity-of-multiple-snps/530/6 "2025-08-04T03:58:13Z")
What is your input size? Mine was 7kb. Not sure if that’s too big. ---
**Author:** ![Steve\_S](https://yyz2.discourse-cdn.com/watermelon/user_avatar/www.alphagenomecommunity.com/steve_s/32/417_2.png) [@Steve\_S](https://www.alphagenomecommunity.com/u/Steve_S)\ **Post date:** [August 5, 2025, 1:36am UTC](https://www.alphagenomecommunity.com/t/using-alphagenome-to-predict-the-cooperativity-of-multiple-snps/530/7 "2025-08-05T01:36:13Z")
never mind, i figured it out