Genetic Testing Laboratories
Most labs that were formerly known for providing specialized Sanger Sequencing now also provide NGS testing as well. Traditionally, genetic testing for Alport Syndrome has been limited to those who had access to Sanger Sequencing labs, but now that NGS has dramatically simplified the process of analyzing genes, Sanger Sequencing has transitioned from being standard to being used primarily for confirming results from NGS analysis. A number of labs that are still actively conducting Sanger Sequencing are listed below. For a comprehensive list of genetic services for Alport Syndrome including NGS and Sanger facilities, visit The American College of Medical Genetics and Genomics; their database is searchable by location, service type, or center name.
University clinics can also be useful resources when considering genetic counseling, and studies involving Alport Syndrome often require and cover costs for genetic testing of willing participants.
Following is a partial list of laboratories that offer genetic testing for Alport syndrome (for a fee). There may be other laboratories of which ASF is unaware.
Detecting Alport Syndrome Genetic Mutations
Because Alport Syndrome is typically genetically heterogeneous (abnormalities occuring on more than one gene), genetic testing for multiple mutations involves various methods. Some known types of genetic variation associated with Alport Syndrome include nonsense variants, exonix deletions/insertions/duplications (also known as copy-number variations CNV’s), mutations located in consensus splicing sites, mutations located out with consensus splicing sites, glycine missense variants in intermediate collagenous domains, and missense variants in non-collagenous domains. Because there are so many possibilities of genetic variance in multiple locations, neither NGS nor Sanger alone can always identify mutations without administering further testing with specialized methods related to suspected mutations. As such, methods for diagnostic testing for Alport Syndrome follow the following procedures.
Next Generation Sequencing Analysis
- Step 1: Targeted Exome Sequensing of COL4A3, COL4A4, and COL4A5
- Step 2: If no pathogenic variant detected, pair analysis for CNVs using Deletion / Duplication (DEL/DUP).
- Step 3: If CNVs are found with DEL/DUP, pair analysis for Multiplex Ligation-Dependant Probe Amplification (MLPA) to confirm CNVs.
- Step 4: If no variants are detected from steps 1-3, conduct RNA sequencing via reverse transcription polymerase chain reaction (PCR) to check for aberrant splicing by intrionic variants.
Sanger Sequencing Analysis
- Step 1: Sanger Sequencing for one or each COL4A3, COL4A4, and/or COL4A5.
- Step 2: If no pathogenic variant detected, pair analysis for MLPA to detect CNVs.
- Step 3: If no variants are detected from MLPA, pair analysis for RNA sequencing.
Some common testing methods for DEL/DUP analysis include Microarray Analysis and VisCap Analysis. PCR tests are for targeted variant analysis. More information on genetic testing methodology can be found at the National Center for Biotechnology Information (NCBI).
When ordering panels for Alport Syndrome, most genetic testing labs have “off the shelf” multigene panels already existing. Gene panels can also be customized by request of a physican, and cost of testing typically depends on how large of a panel is being analyzed. Below are three examples of existing “off the shelf” panels that can identify genetic mutations associated with Alport Syndrome, each with different subsequent testing.