Hi everyone,
We are just starting to look at next gen sequencing for mutation detection and have a lot of questions so I hope to get the current answers and thoughts on here.
Traditionally we use 50k Chips to find a linked region in a family affected with Retinitis Pigmentosa. Then we would simply Sanger sequence the genes in that region to find mutations.
We are hoping that Next Gen will be faster and more efficient and cheaper.
The first problem we have encountered is repeat masking. We hoped to use Agilent eArray to design 75bp pair end long baits to read across our region and then use one of the platforms SOLiD or Illumina to sequence across the region.
We hoped to then use the alignments of the affected vs the unaffected to find putative mutations which would then be tested for segregation and finally against a panel of normals.
however some of our regions are rich in Repeats and the Repeat Maskers are stopping baits designs in that region.
I will post this and many other questions elsewhere in the forum but if someone could recommend a strategy we would be very grateful.
Thanks and its great to be part of this forum
We are just starting to look at next gen sequencing for mutation detection and have a lot of questions so I hope to get the current answers and thoughts on here.
Traditionally we use 50k Chips to find a linked region in a family affected with Retinitis Pigmentosa. Then we would simply Sanger sequence the genes in that region to find mutations.
We are hoping that Next Gen will be faster and more efficient and cheaper.
The first problem we have encountered is repeat masking. We hoped to use Agilent eArray to design 75bp pair end long baits to read across our region and then use one of the platforms SOLiD or Illumina to sequence across the region.
We hoped to then use the alignments of the affected vs the unaffected to find putative mutations which would then be tested for segregation and finally against a panel of normals.
however some of our regions are rich in Repeats and the Repeat Maskers are stopping baits designs in that region.
I will post this and many other questions elsewhere in the forum but if someone could recommend a strategy we would be very grateful.
Thanks and its great to be part of this forum