Cystic Fibrosis ScreeningGuidelines: Laboratory Perspectives

1
Cystic Fibrosis Screening/Guidelines Laboratory
Perspectives

• Jeffrey A. Kant MD PhD
• Director, Division of Molecular Diagnostics
• Professor, Pathology and Human Genetics
• University of Pittsburgh Medical Center

2
ACMG/ACOG CF panel - 2001

• 25 mutations (variants), 0.1 (biased data)
• Did not recommend extended panels unclear
  standard of care and limited yield
• Commercial reagents reopened opportunities for
  screening in many labs
• R117H (also male infertility) reflex testing of
  intron 8 polyT tract to sort out CF-associated
  alleles follow-up family testing for 5T alleles,
  counseling
• Note nomenclature is historical vs. standard
  for some variants (HGVS) transcription start
  site e.g. r.6211GT c.4891GT

3
ACMG/ACOG CF panel - 2004

• 23 variants (2004) clinical sensitivity of 88
  for Caucasian carriers 77 for couples
• Retain R117H with reflex polyT testing because of
  prevalence and significance even though specific
  phenotype may not be predictable
• Deleted 1078delT (
• Deleted I148T (polymorphism occ. associated
  with rare disease-causing variant 3199del6)
• Did NOT add 6 others occurring _at_ 0.10-0.17
• Acknowledged potential local adjustment for
  ethnic background 23-panel detects 49 94

4
Testing Platforms

• Multiple (FDA and ASR/LDT), 10 recent CAP
  survey (arrays, Beads, Invader, mass spec,
  various PCR, rev. hybridization, sequencing)
• Most identify mutations discreetly one 2
  mutations IDd, others as a pool sample
  requires further directed testing for ID
• Some platforms provide genotype information for
  the intron 8 poly T locus only with R117H
  variants (per ACMG/ACOG guidelines)
• Positive controls for all panel variants
  available as purified cell line DNA or synthetic
  substrates

5
Quality CFTR proficiency testing
Purposes Semi-annual assessment per CLIA
(graded), Educational
Poly T locus performance is also quite good
although not reported by all labs or available on
all platforms Source CAP/ACMG MGL2
Proficiency testing module 2006A, 2006B, 2007A
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Quality CFTR proficiency testing
Source CAP/ACMG MGL2 Proficiency testing module
2006A, 2006B, 2007A
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Laboratory Report

• Report is for the Clinician AND patient
• Interpretive and Results sections
• Interpretation
• Negative no mutations identified using a
  recommended mutation screening panel
• Positive (heterozygous) and name of mutation -
  recommend testing partner and/or relatives
• Comment test recommended for carrier testing,
  also useful in patients with suspected CF -
  contact lab
• Early experience with polyT locus genetics
  referral

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Lab Report Results

• Brief background on CF emphasizing carrier rate
  and mutation detection varies by ethnicity there
  IS residual carrier risk with a negative result
• Actual residual risk (1 in X) associated with a
  negative result (paragraph or table with ethnic
  combinations) contact lab for revised residual
  risk in families with undisclosed history of CF
• Methods to include description of panel
  (mutations, polymorphisms, whether poly T locus
  tested and when reported)

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• Sample types (need to validate each)
• Blood, non-invasive samples (buccal brushes,
  saliva)
• Ordering logistics
• Office draw direct to lab with requisition
• Prescription from OB/PCP/PA/NP to patient
• Indication for testing even with best efforts
  not always clear from information received if a
  sample is for screening (possible atypical CF)
• Consent - a process in which the test is one
  part, must be handled by referring healthcare
  professional
• Required by some jurisdictions (documentation)

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Patient and Administrative Issues

• Information to patient (general issue in genetic
  testing)
• Printed materials and consent notwithstanding
• By phone? Follow-up formal genetic counseling?
• Positive screen implications for relatives?
• Confirmatory testing for carrier couples?
• TAT for clinician and patient workload and cost
  implications for laboratories not doing high
  volumes
• Financial
• Coverage/Reimbursement - information is difficult
  to come by in integrated delivery systems
• CPT Coding multiples, MUEs

11

• References
• Grody WW, Cutting GR, Klinger KW, Richards CS,
  Watson MS, Desnick RJ Subcommittee on Cystic
  Fibrosis Screening, Accreditation of Genetic
  Services Committee, ACMG. American College of
  Medical Genetics. Laboratory standards and
  guidelines for population-based cystic fibrosis
  carrier screening. Genet Med 20013149-154.
• Groman, JD, Hefferon, TW, Casals, T et al,
  Variation in a repeat sequence determines whether
  a common variant of the cystic fibrosis
  transmembrane conductance regulator gene is
  pathogenic or benign. Am J Hum Genetic 2004
  741322-1325.
• Strom CM, Huang D, Buller A, Redman J, Crossley
  B, Anderson B, Entwistle T. Sun W. Cystic
  fibrosis screening using the College panel
  platform comparison and lessons learned from the
  first 20,000 samples. Genet Med 20024289-296.
• Watson MS, Cutting GR, Desnick RJ, Driscoll DA,
  Klinger K, Mennuti M, Palomaki GE, Popovich BW,
  Pratt VM, Rohlfs EM, Strom CM, Richards CS, Witt
  DR, Grody WW. Cystic fibrosis population carrier
  screening 2004 revision of American College of
  Medical Genetics mutation panel. Genet Med
  20046387-391
• American College of Medical Genetics, Technical
  Standards and Guidelines for CFTR Mutation
  Testing 2006 Edition (revised 2005)
  http//www.acmg.net/Pages/ACMG_Activities/stds-200
  2/cf.htm
• American College of Medical Genetics, Standards
  and Guidelines for Clinical Genetics
  Laboratories, 2006 Edition http//www.acmg.net/Pa
  ges/ACMG_Activities/stds-2002/g.htm