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Hello everyone,
We have sequenced 5 exomes of patients with rare neurodegenerative disease and for 3 of them we have sequenced their 2 healthy parents as well. Making a total 11 exomes: 5 patients and 6 healthy parents. We have run the raw sequence data using GATK pipeline to find the variants.
We are currently analyzing SNVs that were found in more traditional way using Golden Helix’s SVS: Variants who got high functional score, compound heterozygous, rare recessive, de-novo variants and shared variants. We are trying different filters.
While going in that direction might have potential, we a currently thinking on more holistic analysis for the SNVs results, approach might referred as system-biology or pathway-analysis. Do you have any suggestion where to start, specific software and/or methodologies will be most useful, but general ideas and hints might contribute as well.
Many thanks
Omri
We have sequenced 5 exomes of patients with rare neurodegenerative disease and for 3 of them we have sequenced their 2 healthy parents as well. Making a total 11 exomes: 5 patients and 6 healthy parents. We have run the raw sequence data using GATK pipeline to find the variants.
We are currently analyzing SNVs that were found in more traditional way using Golden Helix’s SVS: Variants who got high functional score, compound heterozygous, rare recessive, de-novo variants and shared variants. We are trying different filters.
While going in that direction might have potential, we a currently thinking on more holistic analysis for the SNVs results, approach might referred as system-biology or pathway-analysis. Do you have any suggestion where to start, specific software and/or methodologies will be most useful, but general ideas and hints might contribute as well.
Many thanks
Omri