Samples are sequenced on the HiSeq X using 150bp, paired end reads. Raw data, or fastq files, are generated using Illumina’s bcl2fastq.
Technical Genome Sequencing
A technical genome is generated for all clinical samples. This consists of a list of all variants detected in the sample, with no interpretation of results or scoring of variants. A report is also included, showing the performance of the sample from a sequencing standpoint and an evaluation of the metrics generated from variant calling. The deliverable file is FASTQ format. A technical genome order returns a vcf and evaluation of metrics.
Interpreted Genome Sequencing
For most clinical cases, an interpreted genome is preferred by practitioners. The interpreted genome has gone through our full clinical pipeline to identify specific variants of interest and which are believed to be disease-causing or related to disease risk. For interpreted genomes, the ordering physician will receive a report that identifies and interprets variants of clinical significance and is signed by a lab director.
It is recommended that genetic counselors be involved in a patient’s decision to have genomic sequencing performed, and also to assist in the interpretation and meaning of results. Genetic counseling costs are not included in the price of whole genome sequencing.
Deliverables to the Physician
BAM file (aligned data)
VCF (variant call format) file
Interpreted report (PDF) signed by medical director or assistant medical director of the CSL
Results Delivered to Ordering Physician
Under the HIPAA Privacy Rule, patients, patient’s designees and patient’s personal representatives can see or be given a copy of the patient’s protected health information, including an electronic copy, with limited exceptions. The patient or the personal representative must put their request in writing and pay for the cost of copying, mailing, or electronic media on which the information is provided. Copies will be sent to the patient within 30 days of his or her request. Clinical Laboratory Improvement Amendments of 1988 (CLIA) regulations to allow laboratories to give a patient, or a person designated by the patient (his or her “personal representative”) access to the patient’s completed test reports on the patient’s or patient’s personal representative’s request.