Targeted Variant Testing

Summary
  • Confirmatory analysis of research or results reported by another laboratory
  • Testing of published founder or common variants
  • Clarification of variant classification for variants reported by another laboratory

With Targeted Variant Testing, you can order for up to 10 variants per order for a fixed price.

Blueprint Genetics will only report the variant(s) of interest. If the individual being tested is suspected of being affected by an inherited disorder then another more comprehensive test (single gene, panel, WES) may be appropriate.

Please contact your local Genetic Services Consultant or our Customer Support team to assist with ordering. We are here to help you!

Availability
4 weeks
Test code
TVT001
* The CPT codes provided are based on AMA guidelines and are for informational purposes only. CPT coding is the sole responsibility of the billing party. Please direct any questions regarding coding to the payer being billed.

Summary

The Blueprint Genetics Targeted Variant Testing (test code TVT001):

Read about our accreditations, certifications and CE-marked IVD medical devices here.

Sample Requirements

  • Blood (min. 1ml) in an EDTA tube
  • Extracted DNA, min. 2 μg in TE buffer or equivalent
  • Saliva (Please see Sample Requirements for accepted saliva kits)

Label the sample tube with your patient’s name, date of birth and the date of sample collection.

We do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue. In addition, if the patient is affected with a hematological malignancy, DNA extracted from a non-hematological source (e.g. skin fibroblasts) is strongly recommended.

Please note that, in rare cases, mitochondrial genome (mtDNA) variants may not be detectable in blood or saliva in which case DNA extracted from post-mitotic tissue such as skeletal muscle may be a better option.

Read more about our sample requirements here.

With Targeted Variant Testing, you can order for up to 10 variants per order for a fixed price.

Blueprint Genetics will only report the variant(s) of interest. If the individual being tested is suspected of being affected by an inherited disorder then another more comprehensive test (single gene, panel, WES) may be appropriate.

Please contact your local Genetic Services Consultant or our Customer Support team to assist with ordering. We are here to help you!

How to order

  • Log in to our online portal Nucleus at nucleus.blueprintgenetics.com for the easiest way to order and access results.
  • Fill out both the consent and requisition forms.
  • Send the sample to Blueprint Genetics.
    • Sample Requirements:
      • Blood (min. 1ml) in an EDTA tube
      • Extracted DNA, min. 2 μg in TE buffer or equivalent
      • Saliva (Oragene DNA OG-500 kit/OGD-500 or OG-575 & OGD-575)
      • Read more about our sample requirements
    • Sending a positive control sample from the index patient is not required.

Methods

Targeted Variant Testing is based on Next Generation Sequencing (NGS) technology and/or Sanger sequencing and qPCR/digital PCR.

Test strengths and limitations

  • CLIA-certified personnel performing clinical testing in a CLIA-certified laboratory
  • Powerful sequencing technologies, advanced target enrichment methods and precision bioinformatics pipelines ensure superior analytical performance
  • High resolution CNV detection included if the index patient’s CNV was diagnosed at Blueprint Genetics
  • Comprehensive clinical statement

Test limitations

CNV analysis and testing of prenatal samples can be done only in cases where the index patient was tested at Blueprint Genetics. Additionally, if you have deep intronic variant detected at another laboratory than Blueprint Genetics, please contact our Support for further information on eligibility.

This test may not reliably detect the following:

  • Low level mosaicism
  • Stretches of mononucleotide repeats
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments

Test Strengths and Limitations

  • CLIA-certified personnel performing clinical testing in a CLIA-certified laboratory
  • Powerful sequencing technologies, advanced target enrichment methods and precision bioinformatics pipelines ensure superior analytical performance
  • High resolution CNV detection included if the index patient’s CNV was diagnosed at Blueprint Genetics
  • Comprehensive clinical statement

Test limitations

Testing of prenatal samples can be done only in cases where the index patient was tested at Blueprint Genetics. Targeted Variant Testing for CNVs is not available for prenatal samples. MtDNA analysis is not available for Targeted Variant Testing. Alu element repeats are not available for testing in cases where the index patient was tested at another laboratory. Structural variant and repeat expansion testing is not available. Additionally, if you have deep intronic variant detected at another laboratory than Blueprint Genetics, please contact our Support for further information on eligibility.

This test may not reliably detect the following:

  • Low level mosaicism
  • Stretches of mononucleotide repeats
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments

Our variant specific tests are sectioned from our high-quality, clinical grade NGS assay. Please see our sequencing and detection performance table for details regarding our ability to detect different types of alterations (Table).

Assays have been validated for various sample types including EDTA-blood, isolated DNA (excluding from formalin fixed paraffin embedded tissue), saliva and dry blood spots (filter cards). These sample types were selected in order to maximize the likelihood for high-quality DNA yield. The diagnostic yield varies depending on the assay used, referring healthcare professional, hospital and country. Plus analysis increases the likelihood of finding a genetic diagnosis for your patient, as large deletions and duplications cannot be detected using sequence analysis alone. Blueprint Genetics’ Plus Analysis is a combination of both sequencing and deletion/duplication (copy number variant (CNV)) analysis.

The performance metrics listed below are from an initial validation performed at our main laboratory in Finland. The performance metrics of our laboratory in Marlborough, MA are equivalent.

Performance of Blueprint Genetics high-quality, clinical grade NGS sequencing assay for panels.

Sensitivity % (TP/(TP+FN) Specificity %
Single nucleotide variants 99.89% (99,153/99,266) >99.9999%
Insertions, deletions and indels by sequence analysis
1-10 bps 99.2% (7,745/7,806) >99.9999%
11-50 bps 99.13% (2,524/2,546) >99.9999%
Copy number variants (exon level dels/dups)
1 exon level deletion (heterozygous) 100% (20/20) NA
1 exon level deletion (homozygous) 100% (5/5) NA
1 exon level deletion (het or homo) 100% (25/25) NA
2-7 exon level deletion (het or homo) 100% (44/44) NA
1-9 exon level duplication (het or homo) 75% (6/8) NA
Simulated CNV detection
5 exons level deletion/duplication 98.7% 100.00%
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb) 100% (25/25)
     
The performance presented above reached by Blueprint Genetics high-quality, clinical grade NGS sequencing assay with the following coverage metrics
     
Mean sequencing depth 143X
Nucleotides with >20x sequencing coverage (%) 99.86%

Performance of Blueprint Genetics Mitochondrial Sequencing Assay.

Sensitivity % Specificity %
ANALYTIC VALIDATION (NA samples; n=4)
Single nucleotide variants
Heteroplasmic (45-100%) 100.0% (50/50) 100.0%
Heteroplasmic (35-45%) 100.0% (87/87) 100.0%
Heteroplasmic (25-35%) 100.0% (73/73) 100.0%
Heteroplasmic (15-25%) 100.0% (77/77) 100.0%
Heteroplasmic (10-15%) 100.0% (74/74) 100.0%
Heteroplasmic (5-10%) 100.0% (3/3) 100.0%
Heteroplasmic (<5%) 50.0% (2/4) 100.0%
CLINICAL VALIDATION (n=76 samples)
All types
Single nucleotide variants n=2026 SNVs
Heteroplasmic (45-100%) 100.0% (1940/1940) 100.0%
Heteroplasmic (35-45%) 100.0% (4/4) 100.0%
Heteroplasmic (25-35%) 100.0% (3/3) 100.0%
Heteroplasmic (15-25%) 100.0% (3/3) 100.0%
Heteroplasmic (10-15%) 100.0% (9/9) 100.0%
Heteroplasmic (5-10%) 92.3% (12/13) 99.98%
Heteroplasmic (<5%) 88.9% (48/54) 99.93%
Insertions and deletions by sequence analysis n=40 indels
Heteroplasmic (45-100%) 1-10bp 100.0% (32/32) 100.0%
Heteroplasmic (5-45%) 1-10bp 100.0% (3/3) 100.0%
Heteroplasmic (<5%) 1-10bp 100.0% (5/5) 99,997%
SIMULATION DATA /(mitomap mutations)
Insertions, and deletions 1-24 bps by sequence analysis; n=17
Homoplasmic (100%) 1-24bp 100.0% (17/17) 99.98%
Heteroplasmic (50%) 100.0% (17/17) 99.99%
Heteroplasmic (25%) 100.0% (17/17) 100.0%
Heteroplasmic (20%) 100.0% (17/17) 100.0%
Heteroplasmic (15%) 100.0% (17/17) 100.0%
Heteroplasmic (10%) 94.1% (16/17) 100.0%
Heteroplasmic (5%) 94.1% (16/17) 100.0%
Copy number variants (separate artifical mutations; n=1500)
Homoplasmic (100%) 500 bp, 1kb, 5 kb 100.0% 100.0%
Heteroplasmic (50%) 500 bp, 1kb, 5 kb 100.0% 100.0%
Heteroplasmic (30%) 500 bp, 1kb, 5 kb 100.0% 100.0%
Heteroplasmic (20%) 500 bp, 1kb, 5 kb 99.7% 100.0%
Heteroplasmic (10%) 500 bp, 1kb, 5 kb 99.0% 100.0%
The performance presented above reached by following coverage metrics at assay level (n=66)
Mean of medians Median of medians
Mean sequencing depth MQ0 (clinical) 18224X 17366X
Nucleotides with >1000x MQ0 sequencing coverage (%) (clinical) 100%
rho zero cell line (=no mtDNA), mean sequencing depth 12X

  • Log in to our online portal Nucleus at nucleus.blueprintgenetics.com for the easiest way to order and access results.
  • Fill out both the consent and requisition forms.
  • Send the sample to Blueprint Genetics.
    • Sample Requirements:
      • Blood (min. 1ml) in an EDTA tube
      • Extracted DNA, min. 2 μg in TE buffer or equivalent
      • Saliva (Oragene DNA OG-500 kit/OGD-500 or OG-575 & OGD-575)
      • Read more about our sample requirements
    • Sending a positive control sample from the index patient is not required.

For samples coming to Helsinki laboratory Targeted Variant Testing is done using Next Generation Sequencing (NGS). When confirmation is required, this is done using Sanger sequencing or dPCR.

For samples coming to Marlborough laboratory Targeted Variant Testing is done with Next Generation Sequencing (NGS) technology and/or Sanger sequencing and dPCR.