Leber Congenital Amaurosis (LCA) is a genetically heterogeneous autosomal recessive disease. There are currently 9 genes that the CNGTL screens for genetic variations associated with LCA: AIPL1, CEP290, CRB1, CRX, GUCY2D, LCA5, RDH12, RPE65 and RPGRIP1. Ninety-three (93) gene segments (out of 177 total segments that make up the complete coding regions of these 9 genes) have been previously reported to harbor disease-causing genetic variations. Certain of these regions are known to harbor more variations than others. In the test offered by the CNGTL, 68 of these gene segments are screened in the order of the likelihood of discovering a genetic variation. These gene segments are screened with a combination of SNPlex and automated DNA sequencing in a carefully crafted balance to result in the most data for the least money. Once a plausible disease-causing genetic variation is identified, the focus of the screening is shifted to the specific gene that harbors the initial plausible disease-causing genetic variation. Patients are only billed for the portion of the test that is completed. As a result, over half of the patients do not reach the upper end of the pricing scale for LCA. These 9 genes are cumulatively responsible for about 70% of LCA cases. The gene segments that are not screened account for less than 1% of LCA alleles that have been discovered to date.
Screening begins with SNPlex by which the individual’s DNA is screened for the 81 most common disease-causing variations. If a variation is discovered with this method of screening we sequence confirm the variation. If no variations are identified we sequence 38 segments of the genes. For any given patient there is 65% likelihood that their DNA will have one or more disease-causing genetic variations discovered in phase 1. Our research and six years of cumulative clinical screening data indicate that 98% of the patients who have currently detectable disease-causing genetic variations in one of these 9 genes will have at least one of their alleles identified in phase 1. After one plausible disease-causing allele is identified in a patient’s DNA, the gene harboring this variation is sequenced to identify the second allele.
Screening includes 17 gene segments. Five percent of patients who do not have a genetic variation identified in phase 1 will have genetic variations detected in phase 2. If a genetic variation is identified in phase 2 the gene that harbors this variation of interest is then sequenced to identify the second allele.
There are a number of options for ordering an LCA test, which patients and physicians may find confusing. Choosing phase 1 followed by phase 2 will allow a patient to be screened for the most likely gene regions to harbor LCA associated genetic variations first. If no variations are identified in phase 1 a preliminary report will be sent to the ordering physician and the lab will proceed with phase 2 testing. Phase 1 only screening allows patients to have their DNA screened more affordably but with the highest likelihood of having a genetic variation identified. Patients and physicians also have the option of choosing one or more specific genes to be screened. Factors that may influence such a choice include: clinical features, family history and treatment potential for specific genes.
Samples from the patient’s parents should also be sent at the same time the patient’s sample is sent. The parental DNA will be screened for all plausible disease-causing genetic variations that are identified in the patient to make sure that variations that we suspect to be responsible for the patient’s disease are inherited in the correct pattern. Screening of the parents is considered a standard part of the patient’s test and is performed at no additional charge.