3 ms·

is the actual basepair sequence shared with the patient? How much of the chromosomal sequence is actually mapped? I'm interested in how this may be incorporat

by blue_eyes1978 7y ago

is the actual basepair sequence shared with the patient? How much of the chromosomal sequence is actually mapped? I'm interested in how this may be incorporated into a patient's chart to fully flush out future diagnoses as sub-clinical symptoms progress down the pathophysiologic maturation chain.

lukasl 7y ago
Great question! In addition to the result report, we share three different types of files with the patient: (1) The FASTQ, which contains the read data from the sequencer (see https://support.illumina.com/bulletins/2016/04/fastq-files-explained.html https://support.illumina.com/bulletins/2016/04/fastq-files-e...) (2) The BAM, which contains sequence alignment data (you can learn more here: https://software.broadinstitute.org/software/igv/BAM https://software.broadinstitute.org/software/igv/BAM) (3) The VCF, which contains the variants present in the patient as compared to the human reference genome We map all >20,000 genes in the human genome, which covers 85% of all known disease-causing mutations. Genes make up about 2% of your DNA. Regarding integrating this into ongoing healthcare for patients: continuous re-analysis of a patient’s genetic data is important, for two reasons: (1) we discover 100-150 new disease-causing genes every year, which means we can return results today that we couldn’t a year ago, and (2) a patient’s symptoms change over time, which matters because we analyze the patient’s DNA for what’s causing their symptoms. Plus, a lot of diseases have a late-onset, which means you might be perfectly fine until your thirties, and all of a sudden you start developing a condition that you didn’t know about. Adult-onset ALD is an example of such a condition (https://www.mayoclinic.org/diseases-conditions/adrenoleukodystrophy/symptoms-causes/syc-20369157 https://www.mayoclinic.org/diseases-conditions/adrenoleukody...).

lukasl 7y ago

Great question! In addition to the result report, we share three different types of files with the patient: (1) The FASTQ, which contains the read data from the sequencer (see https://support.illumina.com/bulletins/2016/04/fastq-files-explained.html https://support.illumina.com/bulletins/2016/04/fastq-files-e...) (2) The BAM, which contains sequence alignment data (you can learn more here: https://software.broadinstitute.org/software/igv/BAM https://software.broadinstitute.org/software/igv/BAM) (3) The VCF, which contains the variants present in the patient as compared to the human reference genome We map all >20,000 genes in the human genome, which covers 85% of all known disease-causing mutations. Genes make up about 2% of your DNA. Regarding integrating this into ongoing healthcare for patients: continuous re-analysis of a patient’s genetic data is important, for two reasons: (1) we discover 100-150 new disease-causing genes every year, which means we can return results today that we couldn’t a year ago, and (2) a patient’s symptoms change over time, which matters because we analyze the patient’s DNA for what’s causing their symptoms. Plus, a lot of diseases have a late-onset, which means you might be perfectly fine until your thirties, and all of a sudden you start developing a condition that you didn’t know about. Adult-onset ALD is an example of such a condition (https://www.mayoclinic.org/diseases-conditions/adrenoleukodystrophy/symptoms-causes/syc-20369157 https://www.mayoclinic.org/diseases-conditions/adrenoleukody...).