Blueprint Genetics

A study of 183 index patients demonstrates enhanced diagnostic performance of NGS-based panel testing including the PKD1 gene

Apr 04, 2019

The diagnostic yield of genetic testing in a phenotypically heterogeneous cohort of 183 patients with cystic kidney disease was 54%. Almost 2 out of 3 disease-causing variants were identified in PKD1, a particularly difficult-to-sequence gene.

Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited kidney disease, caused primarily by variants in two genes, PKD1 and PKD2. A recent study by Blueprint Genetics suggests that technological advances in the ability to analyze the difficult-to-sequence PKD1 gene leads to a higher diagnostic yield, and therefore significantly improves the management of patients and families with ADPKD.

“It has been exciting to see how next generation sequencing (NGS) can be harnessed to reliably diagnose variants in PKD1 gene. Our tailored sequencing, bioinformatics and interpretation strategies for PKD1 analysis are now making it possible to move away from the original expensive and labor-intensive “gold standard” testing method, which was long-range PCR and Sanger based diagnostics. In addition to our customized NGS platform, we have developed specific Sanger sequencing approaches to supplement and confirm NGS test results”, says Chief Medical Officer Tero-Pekka Alastalo (MD, PhD).

Blueprint Genetics’ panels dissected from a high quality NGS whole exome sequencing platform bring additional value to ADPKD patients and health care providers. A single test includes copy number variant detection, analysis of clinically relevant deep intronic variants and covers a wide range of differential diagnoses.

PKD1 is technically very challenging to analyze due to its large size, high GC-content and duplication of the first 33 exons with a high degree of homology (90-99% identity) to six nearby pseudogenes (PKD1 P1–P6). In the validation study, Blueprint Genetics has demonstrated the following performance metrics:

  • Overall high mean coverage (205x)
  • 100% of the target nucleotides covered at least 20x with a mapping quality threshold of 20
  • 99.5% of target nucleotides covered at least 20x with mapping quality threshold of 40

In the study, 81% of the diagnostic PKD1 variants were detected in the duplicated region and were all further confirmed by a custom designed Sanger sequencing approach, thus demonstrating a very high confidence in differentiating PKD1 reads from the pseudogene reads.

“Additional confidence of the test was shown by analyzing 10 patients with polycystic kidney disease who had prior negative NGS-based genetic testing. In 7 of these 10 patients, previously undetected PKD1 variants in the duplicated region were identified. I think we can say with confidence, that PKD1 variant detection with NGS is now possible, if a high-quality assay is used. However, not all NGS approaches are there yet – it is important to understand and inquire about a test’s limitations, strengths and whether an analytic validation has been performed”, Alastalo continues.

Summary of results:

  • An unselected cohort of patients with cystic kidney disease were analyzed using Blueprint Genetics’ Polycystic Kidney Disease or Cystic Kidney Disease Panels, which include a total of 42 genes.
  • The diagnostic yield in this cohort was 54%
  • 7% of patients with a diagnostic test result had a pathogenic or likely pathogenic copy number variant in the HNF1B, PKD1 and NPHP1 genes
  • 63% of patients with a diagnostic finding had a disease-causing variant in the PKD1 gene; 81% of PKD1 variants were in the duplicated region
  • The majority of the diagnostic PKD1 variants were single base-pair substitutions including 40% missense and 26% nonsense variants
  • Diagnostic variants were identified in 11 different genes, further highlighting the heterogeneity of the cohort

Read more about the study here.

Further information:
Chief Medical Officer Tero-Pekka Alastalo, tero-pekka.alastalo@blueprintgenetics.com
Communication manager Juulia Simonen, juulia.simonen@blueprintgenetics.com.

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