Newborn Screening Is on a Collision Course with Public Health Ethics.

Newborn screening was established over 50 years ago to identify cases of disorders that were serious, urgent, and treatable, mirroring the criteria of Wilson and Jungner. In the last decade, conditions have been added to newborn screening that do not strictly meet these criteria, and genomic newborn screening is beginning to be discussed. Some of these new and proposed additions to newborn screening entail serious public health ethical issues that need to be explored.

Newborn screening for neurodevelopmental diseases: Are we there yet?

In the US, newborn screening (NBS) is a unique health program that supports health equity and screens virtually every baby after birth, and has brought timely treatments to babies since the 1960's. With the decreasing cost of sequencing and the improving methods to interpret genetic data, there is an opportunity to add DNA sequencing as a screening method to facilitate the identification of babies with treatable conditions that cannot be identified in any other scalable way, including highly penetrant genetic neurodevelopmental disorders (NDD). However, the lack of effective dietary or drug-based treatments has made it nearly impossible to consider NDDs in the current NBS framework, yet it is anticipated that any treatment will be maximally effective if started early. Hence there is a critical need for large scale pilot studies to assess if and how NDDs can be effectively screened at birth, if parents desire that information, and what impact early diagnosis may have. Here we attempt to provide an overview of the recent advances in NDD treatments, explore the possible framework of setting up a pilot study to genetically screen for NDDs, highlight key technical, practical, and ethical considerations and challenges, and examine the policy and health system implications.

A Novel Approach to Improve Newborn Screening for Congenital Hypothyroidism by Integrating Covariate-Adjusted Results of Different Tests into CLIR Customized Interpretive Tools.

Newborn screening for congenital hypothyroidism remains challenging decades after broad implementation worldwide. Testing protocols are not uniform in terms of targets (TSH and/or T4) and protocols (parallel vs. sequential testing; one or two specimen collection times), and specificity (with or without collection of a second specimen) is overall poor. The purpose of this retrospective study is to investigate the potential impact of multivariate pattern recognition software (CLIR) to improve the post-analytical interpretation of screening results. Seven programs contributed reference data (N = 1,970,536) and two sets of true (TP, N = 1369 combined) and false (FP, N = 15,201) positive cases for validation and verification purposes, respectively. Data were adjusted for age at collection, birth weight, and location using polynomial regression models of the fifth degree to create three-dimensional regression surfaces. Customized Single Condition Tools and Dual Scatter Plots were created using CLIR to optimize the differential diagnosis between TP and FP cases in the validation set. Verification testing correctly identified 446/454 (98%) of the TP cases, and could have prevented 1931/5447 (35%) of the FP cases, with variable impact among locations (range 4% to 50%). CLIR tools either as made here or preferably standardized to the recommended uniform screening panel could improve performance of newborn screening for congenital hypothyroidism.

Twin chorionicity and zygosity both vary with maternal age.

Objective: To determine the ratio of dichorionic (DC) to monochorionic (MC) twins by maternal age. Methods: We reviewed all twin pregnancies undergoing first trimester screening (FTS) with nuchal translucency from April 2009 to December 2012 with sonographic determination of chorionicity. Cases were linked to newborn screening (NBS) results and zygosity estimated based on rates of fetal sex discordance. The ratio of DC to MC placentation by maternal age was calculated. Results: We identified 11,351 twin pregnancies with FTS and documented chorionicity. Among these, 7,861 (64.2%) had linked data on FTS and NBS to allow estimation of zygosity based on neonatal sex. Of these, 1,464 (18.6%) were MC and 6,406 (81.4%) DC. The MC twin rate remained constant while the DC twin rate increased with maternal age until 40y. At < 20y, 55% of twin pregnancies were monozygotic (MZ), as compared to 29% at ≥ 40y. Of MZ twins, 38% were DC at < 20y, while 53% were DC at ≥ 40y. Conclusions: Our data suggest a relationship of both zygosity and chorionicity with maternal age. DZ twinning increased with maternal age, while among MZ twins, the proportion that were DC also increased with maternal age.

The role of exome sequencing in newborn screening for inborn errors of metabolism.

Public health newborn screening (NBS) programs provide population-scale ascertainment of rare, treatable conditions that require urgent intervention. Tandem mass spectrometry (MS/MS) is currently used to screen newborns for a panel of rare inborn errors of metabolism (IEMs)1-4. The NBSeq project evaluated whole-exome sequencing (WES) as an innovative methodology for NBS. We obtained archived residual dried blood spots and data for nearly all IEM cases from the 4.5 million infants born in California between mid-2005 and 2013 and from some infants who screened positive by MS/MS, but were unaffected upon follow-up testing. WES had an overall sensitivity of 88% and specificity of 98.4%, compared to 99.0% and 99.8%, respectively for MS/MS, although effectiveness varied among individual IEMs. Thus, WES alone was insufficiently sensitive or specific to be a primary screen for most NBS IEMs. However, as a secondary test for infants with abnormal MS/MS screens, WES could reduce false-positive results, facilitate timely case resolution and in some instances even suggest more appropriate or specific diagnosis than that initially obtained. This study represents the largest, to date, sequencing effort of an entire population of IEM-affected cases, allowing unbiased assessment of current capabilities of WES as a tool for population screening.

Genomic Analysis of Historical Cases with Positive Newborn Screens for Short-Chain Acyl-CoA Dehydrogenase Deficiency Shows That a Validated Second-Tier Biochemical Test Can Replace Future Sequencing.

Short-chain acyl-CoA dehydrogenase deficiency (SCADD) is a rare autosomal recessive disorder of ß-oxidation caused by pathogenic variants in the ACADS gene. Analyte testing for SCADD in blood and urine, including newborn screening (NBS) using tandem mass spectrometry (MS/MS) on dried blood spots (DBSs), is complicated by the presence of two relatively common ACADS variants (c.625G>A and c.511C>T). Individuals homozygous for these variants or compound heterozygous do not have clinical disease but do have reduced short-chain acyl-CoA dehydrogenase (SCAD) activity, resulting in elevated blood and urine metabolites. As part of a larger study of the potential role of exome sequencing in NBS in California, we reviewed ACADS sequence and MS/MS data from DBSs from a cohort of 74 patients identified to have SCADD. Of this cohort, approximately 60% had one or more of the common variants and did not have the two rare variants, and thus would need no further testing. Retrospective analysis of ethylmalonic acid, glutaric acid, 2-hydroxyglutaric acid, 3-hydroxyglutaric acid, and methylsuccinic acid demonstrated that second-tier testing applied before the release of the newborn screening result could reduce referrals by over 50% and improve the positive predictive value for SCADD to above 75%.

The utility of nuchal translucency ultrasound in identifying rare chromosomal abnormalities not detectable by cell-free DNA screening.

OBJECTIVE: To evaluate the utility of nuchal translucency (NT) screening in the detection of rare chromosomal aneuploidies in the setting of cell-free DNA (cfDNA). METHODS: A retrospective cohort study of pregnancies screened through the California Prenatal Screening Program between March 2009 and December 2012. Karyotype analysis was the primary method of chromosomal evaluation during the study period and abnormal chromosomal karyotype results were classified by whether the abnormality would be detectable by cfDNA (nonmosaic trisomy 13, 18, 21 or sex-chromosomal aneuploidy [SCA]). For those rare aneuploidies detectable by karyotype but not cfDNA, the number of cases that had an increased NT and the detection rate and positive predictive value (PPV) of increased NT for rare aneuploidies were determined. RESULTS: A total of 452 901 pregnant women had screening. There were 2572 chromosomally abnormal fetuses, of which 1922 (74.7%) had a common aneuploidy detectable by cfDNA, leaving 450 979 without T13, 18, 21. Of these, 4181 (0.93%) had an NT ≥3.0 mm. There were 649 rare aneuploidies not detectable by cfDNA. Of these, 108 (16.6%) had an NT ≥3.0 mm. The PPV of an NT ≥3.0 mm for rare aneuploidies was 2.6%. In all, 4176 fetuses need to be screened with NT to detect a rare aneuploidy. CONCLUSIONS: The addition of NT to cfDNA screening would detect 16.6% of rare aneuploidies. Increased NT has a low PPV for rare aneuploidies and a large number of women would need NT screening to detect each affected fetus.

Reference intervals for lymphocyte subsets in preterm and term neonates without immune defects.

BACKGROUND: In 6.5 years of newborn screening for severe combined immunodeficiency in California, 3,252,156 infants had DNA from dried blood spots (DBSs) assayed for T-cell receptor excision circles. Infants with T-cell receptor excision circle values of less than a designated cutoff on a single DBS, 2 DBS samples with insufficient PCR amplification, or known genetic risk of immunodeficiency had peripheral blood complete blood counts and lymphocyte subsets assayed in a single flow cytometry laboratory. Cases in which immune defects were ruled out were available for analysis. OBJECTIVE: We sought to determine reference intervals for lymphocyte subsets in racially/ethnically diverse preterm and term newborns who proved to be unaffected by any T-lymphopenic immune disorder. METHODS: Effective gestational age (GA) was defined as GA at birth plus postnatal age at the time of sample collection. After determining exclusion criteria, we analyzed demographic and clinical information, complete and differential white blood cell counts, and lymphocyte subsets for 301 infants, with serial measurements for 33 infants. Lymphocyte subset measurements included total T cells, helper and cytotoxic T-cell subsets, naive and memory phenotype of each T-cell subset, B cells, and natural killer cells. RESULTS: Reference intervals were generated for absolute numbers and lymphocyte subsets from infants with effective GAs of 22 to 52 weeks. Sex and ethnicity were not significant determinants of lymphocyte subset counts in this population. Lymphocyte counts increased postnatally. CONCLUSION: This study provides a baseline for interpreting comprehensive lymphocyte data in preterm and term infants, aiding clinicians to determine which newborns require further evaluations for immunodeficiency.

Newborn Screening for Severe Combined Immunodeficiency and T-cell Lymphopenia in California, 2010-2017.

OBJECTIVES: Newborn screening for severe combined immunodeficiency (SCID) was instituted in California in 2010. In the ensuing 6.5 years, 3 252 156 infants in the state had DNA from dried blood spots assayed for T-cell receptor excision circles (TRECs). Abnormal TREC results were followed-up with liquid blood testing for T-cell abnormalities. We report the performance of the SCID screening program and the outcomes of infants who were identified. METHODS: Data that were reviewed and analyzed included demographics, nursery summaries, TREC and lymphocyte flow-cytometry values, and available follow-up, including clinical and genetic diagnoses, treatments, and outcomes. RESULTS: Infants with clinically significant T-cell lymphopenia (TCL) were successfully identified at a rate of 1 in 15 300 births. Of these, 50 cases of SCID, or 1 in 65 000 births (95% confidence interval 1 in 51 000-1 in 90 000) were found. Prompt treatment led to 94% survival. Infants with non-SCID TCL were also identified, diagnosed and managed, including 4 with complete DiGeorge syndrome who received thymus transplants. Although no cases of typical SCID are known to have been missed, 2 infants with delayed-onset leaky SCID had normal neonatal TREC screens but came to clinical attention at 7 and 23 months of age. CONCLUSIONS: Population-based TREC testing, although unable to detect immune defects in which T cells are present at birth, is effective for identifying SCID and clinically important TCL with high sensitivity and specificity. The experience in California supports the rapid, widespread adoption of SCID newborn screening.

Single-Gene Sequencing in Newborn Screening: Success, Challenge, Hope.

Some state-based newborn screening programs in the United States already use sequencing technology, as a secondary screening test for individual conditions rather than as a broad screening tool. Newborn screening programs sequence an individual gene, such as the cystic fibrosis transmembrane conductance regulator, which causes cystic fibrosis, after an initial biochemical test suggests that a baby might have a condition related to that gene. The experiences of state public health departments with individual-gene sequencing illustrate both the usefulness of the technology and its complexities. Here I discuss how newborn screening programs investigate cystic fibrosis and, as another example, adrenoleukodystrophy through individual gene sequencing.

Whole exome and whole genome sequencing with dried blood spot DNA without whole genome amplification.

Newborn screening (NBS) for rare conditions is performed in all 50 states in the USA. We have partnered with the California Department of Public Health Genetic Disease Laboratory to determine whether sufficient DNA can be extracted from archived dried blood spots (DBS) for next-generation sequencing in the hopes that next-generation sequencing can play a role in NBS. We optimized the DNA extraction and sequencing library preparation protocols for residual infant DBS archived over 20 years ago and successfully obtained acceptable whole exome and whole genome sequencing data. This sequencing study using DBS DNA without whole genome amplification prior to sequencing library preparation provides evidence that properly stored residual newborn DBS are a satisfactory source of DNA for genetic studies.

Genomic sequencing in cystic fibrosis newborn screening: what works best, two-tier predefined CFTR mutation panels or second-tier CFTR panel followed by third-tier sequencing?

PurposeThe purpose of this study was to model the performance of several known two-tier, predefined mutation panels and three-tier algorithms for cystic fibrosis (CF) screening utilizing the ethnically diverse California population.MethodsThe cystic fibrosis transmembrane conductance regulator (CFTR) mutations identified among the 317 CF cases in California screened between 12 August 2008 and 18 December 2012 were used to compare the expected CF detection rates for several two- and three-tier screening approaches, including the current California approach, which consists of a population-specific 40-mutation panel followed by third-tier sequencing when indicated.ResultsThe data show that the strategy of using third-tier sequencing improves CF detection following an initial elevated immunoreactive trypsinogen and detection of only one mutation on a second-tier panel.ConclusionIn a diverse population, the use of a second-tier panel followed by third-tier CFTR gene sequencing provides a better detection rate for CF, compared with the use of a second-tier approach alone, and is an effective way to minimize the referrals of CF carriers for sweat testing. Restricting screening to a second-tier testing to predefined mutation panels, even broad ones, results in some missed CF cases and demonstrates the limited utility of this approach in states that have diverse multiethnic populations.

Newborn Sequencing in Genomic Medicine and Public Health.

The rapid development of genomic sequencing technologies has decreased the cost of genetic analysis to the extent that it seems plausible that genome-scale sequencing could have widespread availability in pediatric care. Genomic sequencing provides a powerful diagnostic modality for patients who manifest symptoms of monogenic disease and an opportunity to detect health conditions before their development. However, many technical, clinical, ethical, and societal challenges should be addressed before such technology is widely deployed in pediatric practice. This article provides an overview of the Newborn Sequencing in Genomic Medicine and Public Health Consortium, which is investigating the application of genome-scale sequencing in newborns for both diagnosis and screening.

Observed Rate of Down Syndrome in Twin Pregnancies.

OBJECTIVE: To evaluate the observed incidence of Down syndrome in twins compared with that expected based on maternal age-matched singletons, which is the current clinical approach. METHODS: This was a retrospective review of California Prenatal Screening Program participants with expected delivery dates between July 1995 and December 2012. Cases confirmed prenatally or postnatally with a genetic imbalance leading to phenotypic Down syndrome (trisomy 21, mosaic trisomy 21, or translocations) were included. Pregnancies conceived with ovum donation and women older than 45 years were excluded. We compared the observed Down syndrome incidence per pregnancy for twins with expected incidence by extrapolating from singleton data and expected zygosity as is the current clinical approach. This extrapolation assumes that monozygotic pregnancies have equivalent Down syndrome risk per pregnancy relative to maternal age-matched singletons and dizygotic pregnancies have twice the risk of at least one affected fetus. Zygosity for affected cases was presumed to be monozygotic with Down syndrome concordance and dizygotic with Down syndrome discordance. Counts were compared using cumulative Poisson distributions. RESULTS: Of 77,279 twin pregnancies, 182 (0.2%) had at least one fetus with Down syndrome confirmed by karyotype. The ratio of observed-to-expected Down syndrome incidence per pregnancy was 33.6%, 75.2%, and 70.0% for monozygotic, dizygotic, and all twins, respectively (P<.001 for all comparisons). Considering maternal age subgroups and twin zygosity, a significantly lower-than-expected Down syndrome incidence was seen for women aged 25 to 45 years with monozygotic pregnancies and overall for women aged 25 to 45 years with dizygotic pregnancies. CONCLUSION: The observed incidence of Down syndrome in twin pregnancies is lower than expected, most notably for monozygotic pregnancies and with increasing maternal age. Risk-based counseling can strongly affect women's choices regarding testing and management during pregnancy, so an understanding of the true Down syndrome risk in twin gestations is crucial.

Recurrence of Preterm Birth and Early Term Birth.

OBJECTIVE: To examine recurrent preterm birth and early term birth in women's initial and immediately subsequent pregnancies. METHODS: This retrospective cohort study included 163,889 women who delivered their first and second liveborn singleton neonates between 20 and 44 weeks of gestation in California from 2005 through 2011. Data from hospital discharge records and birth certificates were used for analyses. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using logistic regression models adjusted for risk factors. RESULTS: Shorter gestational duration in the first pregnancy increased the risk of subsequent preterm birth (both early, before 32 weeks of gestation, and later, from 32 to 36 weeks of gestation) as well as early term birth (37-38 weeks of gestation). Compared with women with a prior term birth, women with a prior early preterm birth (before 32 weeks of gestation) were at the highest risk for a subsequent early preterm birth (58/935 [6.2%] compared with 367/118,505 [0.3%], adjusted OR 23.3, 95% CI 17.2-31.7). Women with a prior early term birth had more than a twofold increased risk for subsequent preterm birth (before 32 weeks of gestation: 171/36,017 [0.5%], adjusted OR 2.0, 95% CI 1.6-2.3; from 32 to 36 weeks of gestation: 2,086/36,017 [6.8%], adjusted OR 3.0, 95% CI 2.9-3.2) or early term birth (13,582/36,017 [37.7%], adjusted OR 2.2, 95% CI 2.2-2.3). CONCLUSION: Both preterm birth and early term birth are associated with these outcomes in a subsequent pregnancy. Increased clinical attention and research efforts may benefit from a focus on women with a prior early term birth as well as those with prior preterm birth.

First trimester pregnancy-associated plasma protein-A and birth weight.

OBJECTIVE: To evaluate first trimester pregnancy-associated plasma protein-A (PAPP-A) and birth weight percentile. STUDY DESIGN: Included were women who underwent first trimester prenatal screening through the California Prenatal Screening Program with expected dates of delivery between August 2009 and December 2010, linked birth certificate and hospital discharge records, known birth weight, and no chromosomal abnormality (n=134.105). PAPP-A results were reported as multiples of the median. The frequency of small or large for gestational age (SGA, ≤10%; LGA, ≥90%) versus appropriately grown for gestational age birth was examined by PAPP-A percentile. Patterns were studied by gestational age at delivery. Relative risks (RRs) and their 95% confidence intervals were adjusted for race/ethnicity. RESULTS: Women with PAPP-A ≤10th percentile and an infant born after 32 weeks were increasingly more likely to have an SGA infant (adjRRs 1.5-4.6) as the PAPP-A percentile declined, and were increasingly less like to have an LGA infant born at term (adjRRs 0.5-0.7) compared to women with PAPP-A measurement >10th to <90th percentile. PAPP-A ≥90th percentile was protective for SGA among infants born after 32 weeks gestation (adjRRs 0.3-0.7) and was associated with LGA among infants born at term (adjRRs 1.2-8.2). CONCLUSION: Women with PAPP-A ≤10th percentile are more likely to have an SGA infant at all gestational ages. PAPP-A ≥90th percentile is protective against SGA and is associated with an increased risk of LGA for infants born after 32 weeks gestation.

Cell-free DNA vs sequential screening for the detection of fetal chromosomal abnormalities.

BACKGROUND: Sequential and cell-free DNA (cfDNA) screening are both tests for the common aneuploidies. Although cfDNA has a greater detection rate (DR) for trisomy 21, sequential screening also can identify risk for other aneuploidies. The comparative DR for all chromosomal abnormalities is unknown. OBJECTIVE: To compare sequential and cfDNA screening for detection of fetal chromosomal abnormalities in a general prenatal cohort. STUDY DESIGN: The performance of sequential screening for the detection of chromosome abnormalities in a cohort of patients screened through the California Prenatal Screening Program with estimated due dates between August 2009 and December 2012 was compared with the estimated DRs and false-positive rates (FPRs) of cfDNA screening if used as primary screening in this same cohort. DR and FPR for cfDNA screening were abstracted from the published literature, as were the rates of "no results" in euploid and aneuploid cases. Chromosome abnormalities in the entire cohort were categorized as detectable (trisomies 13, 18, and 21, and sex chromosome aneuploidy), or not detectable (other chromosome abnormalities) by cfDNA screening. DR and FPR were compared for individual and all chromosome abnormalities. DR and FPR for the cohort were compared if "no results" cases were considered "screen negative" or "screen positive" for aneuploidy. DR and FPR rates were compared by use of the Fisher exact test. RESULTS: Of 452,901 women who underwent sequential screening during the time period of the study, 2575 (0.57%) had a fetal chromosomal abnormality; 2101 were detected for a DR of 81.6%, and 19,929 euploid fetuses had positive sequential screening for an FPR rate of 4.5%. If no results cases were presumed normal, cfDNA screening would have detected 1820 chromosome abnormalities (70.7%) with an FPR of 0.7%. If no results cases were considered screen positive, 1985 (77.1%) cases would be detected at a total screen positive rate of 3.7%. In either case, the detection rate of sequential screening for all aneuploidies in the cohort was greater than cfDNA (P<.0001). CONCLUSION: For primary population screening, cfDNA provides lower DR than sequential screening if considering detection of all chromosomal abnormalities. Assuming that no results cfDNA cases are high-risk improves cfDNA detection but with a greater FPR. cfDNA should not be adopted as primary screening without further evaluation of the implications for detection of all chromosomal abnormalities and how to best evaluate no results cases.

Damaged goods?: an empirical cohort study of blood specimens collected 12 to 23 hours after birth in newborn screening in California.

PURPOSE: The current Clinical and Laboratory Standards Institute standard recommends blood collection from 24 to 48 hours after birth for newborn genetic disorder screening. We used California population-level data to determine whether early specimens (collected from 12 to 23 hours) would also be considered satisfactory based on screening performance. METHODS: Screening data from California Genetic Disease Screening Program were analyzed for false-negative and false-positive rates in four disease categories: metabolic disorders detectable by tandem mass spectrometry (MS/MS); congenital adrenal hyperplasia (CAH); congenital hypothyroidism (CH); and initial immune reactive trypsinogen (IRT) for cystic fibrosis (CF). We compared the rates between the early-collection group (12 to 23 hours) and the standard-collection group (24 to 48 hours). RESULTS: No significant difference of false-negative rate was detected between the two collection-timing groups. Early specimens had a significantly higher false-positive rate for CH (0.10 vs. 0.01%) and IRT (1.85 vs. 1.54%) but a lower false-positive rate for MSMS metabolic disorders (0.11 vs. 0.18%) and CAH (0.10 vs. 0.14%). CONCLUSION: Newborn specimens collected after 12 hours provided satisfactory screening performance. A policy allowing earlier collection could improve timeliness of reporting screening results.

Detection Rates for Aneuploidy by First-Trimester and Sequential Screening.

OBJECTIVE: To estimate detection rates for aneuploidy by first-trimester and sequential screening. METHODS: The study included women with singleton pregnancies who participated in the California Prenatal Screening Program with estimated delivery dates from August 2009 to December 2012 who had first- or first- and second-trimester (sequential) screening. Detection rates were measured for target (trisomies 21 and 18) and other aneuploidies identified from the California Chromosome Defect Registry. RESULTS: Of 452,901 women screened, 17,435 (3.8%) were screen-positive for Down syndrome only; 433 (0.1%) for trisomy 18 only; 1,689 (0.4%) for both Down syndrome and trisomy 18; and 2,947 (0.7%) for neural tube defects, Smith-Lemli-Opitz syndrome, or for multiple conditions. The detection rates were Down syndrome-92.9% (95% confidence interval [CI] 91.4-94.2); trisomy 18-93.2% (95% CI 90.5-95.9); trisomy 13-80.4% (95% CI 73.9-86.9); 45,X-80.1% (95% CI 73.9-86.3), and triploidy-91.0% (95% CI 84.2-97.9). Overall, the detection rate for chromosome abnormalities was 81.6% (95% CI 80.0-83.1) at an overall false-positive rate of 4.5%. CONCLUSION: First-trimester and sequential screening are sensitive and specific for the broad range of karyotype abnormalities seen in the population. LEVEL OF EVIDENCE: II.