Refinement of newborn screening for cystic fibrosis with next generation sequencing

Abstract

Background Newborn screening for cystic fibrosis (CF) has been underway universally in the United States for more than a decade, as well in most European countries, and algorithms have been evolving throughout this period with quality improvement projects as immunoreactive trypsinogen (IRT) determinations alone have been transformed to a 2‐tier strategy with DNA analyses. Objective To apply next generation sequencing (NGS) as a screening method to expand the DNA tier and identify substantially more variants in the CF transmembrane conductance regulator (CFTR) gene to enhance sensitivity and equity while minimizing incidental findings. Design Sequential evaluation and improvement plan in three phases using algorithm modifications coupled to statewide follow up and analysis of screening outcomes. Results After demonstrating feasibility in the first phase, we studied an IRT/NGS algorithm that included CFTR Variants with Varying Clinical Consequences (VVCCs). This revealed a high identification of CF patients with 2‐variants detected through screening, but for every CF case there were 1.4 with CF metabolic syndrome/CF screen positive, inconclusive diagnosis (CRMS/CFSPID). This led us to a third phase of improvement in which the VVCCs were eliminated except for R117H, resulting in 94% 2‐variant detection of patients and 0.44:1 ratio of CRMS/CFSPID to CF. Conclusion NGS can be used with IRT as an effective method of identifying infants at risk for CF without an appreciable increase in detection of carriers. Its potential added value includes facilitating equity, enhancing sensitivity and detecting more CF patients with 2‐variants during the screening process.

Children with cystic fibrosis are still receiving inconclusive diagnosis despite undergoing newborn screening

“…The decrease in CRMS/CFSPID cases was accompanied by a decrease in sensitivity and positive predictive value of the programme 15 . A study from Wisconsin showed that when the NBS algorithm included CFTR variants with varying clinical consequences (VVCCs), the ratio of CRMS/CFSPID to CF cases was 1.4:1 16 . After excluding VVCCs, except for R117H, the analysis indicated a decrease in the number of patients with two variants.…”

“…15 A study from Wisconsin showed that when the NBS algorithm included CFTR variants with varying clinical consequences (VVCCs), the ratio of CRMS/CFSPID to CF cases was 1.4:1. 16 After excluding VVCCs, except for R117H, the analysis indicated a decrease in the number of patients with two variants. Specifically, of the 18 infants diagnosed with CF, only 17 (94%) had two pathogenic variants.…”

Severe lung disease in children with cystic fibrosis missed in newborn screening

“…The CF NBS algorithms used in the United States 14 are quite variable, particularly the IRT cutoff values employed and a number of variants in CFTR panels, but as knowledge and technologies have increased, 16–18 better tests have emerged 3 . Once a region like New Jersey begins with a screening protocol, however, it is difficult to change as other screening methods evolve.…”

“…Cystic fibrosis (CF), a common, life‐shortening, autosomal recessive genetic disorder caused by pathogenic variants in the cystic fibrosis transmembrane conductance regulator ( CFTR ) that can be detected through newborn screening (NBS). All CF NBS methods begin with the biomarker immunoreactive trypsinogen (IRT) 1–3 . Although IRT followed by a second IRT to confirm hypertrypsinogenemia was the original screening test applied to dried blood spot specimens, 4,5 this method was supplanted in 1993 when Gregg et al 5 reported the IRT/DNA(F508del) algorithm that resolved the problems with IRT described by Rock et al 6 After Farrell et al 7 reported significant nutritional benefits of early diagnosis through NBS, as established in a randomized clinical trial, New Jersey implemented CF NBS in 2001 with IRT/DNA (F508del), the standard method of that time 8 .…”

“…The most striking feature of some cases was their clinically significant/severe lung disease. In an effort to support quality improvement with a change to the better CF NBS methods that had evolved, 3 we reviewed these cases in detail and are reporting herein summaries that illustrate the life‐threatening risks that can develop in patients with delayed diagnoses.…”