ARTICLE Interpretation of Genomic Sequencing Results in Healthy and Ill Newborns: Results from the BabySeq Project Ozge Ceyhan-Birsoy,1,2 Jaclyn B. Murry,2,4 Kalotina Machini,2,4 Matthew S. Lebo,2,3,4,11 Timothy W. Yu,4,5,6 Shawn Fayer,7 Casie A. Genetti,5 Talia S. Schwartz,5 Pankaj B. Agrawal,4,5,8 Richard B. Parad,4,9 Ingrid A. Holm,4,5 Amy L. McGuire,10 Robert C. Green,4,7,11 Heidi L. Rehm,2,3,4,11,12 Alan H. Beggs,4,5,* and The BabySeq Project Team Genomic sequencing provides many opportunities in newborn clinical care, but the challenges of interpreting and reporting newborn genomic sequencing (nGS) results need to be addressed for its broader and effective application. The BabySeq Project is a pilot random- ized clinical trial that explores the medical, behavioral, and economic impacts of nGS in well newborns and those admitted to a neonatal intensive care unit (NICU). Here we present childhood-onset and actionable adult-onset disease risk, carrier status, and pharmacoge- nomics findings from nGS of 159 newborns in the BabySeq Project. nGS revealed a risk of childhood-onset disease in 15/159 (9.4%) newborns; none of the disease risks were anticipated based on the infants’ known clinical or family histories. nGS also revealed action- able adult-onset disease risk in 3/85 (3.5%) newborns whose parents consented to receive this information. Carrier status for recessive diseases and pharmacogenomics variants were reported in 88% and 5% of newborns, respectively. Additional indication-based analyses were performed in 29/32 (91%) NICU newborns and 6/127 (5%) healthy newborns who later had presentations that prompted a diag- nostic analysis. No variants that sufficiently explained the reason for the indications were identified; however, suspicious but uncertain results were reported in five newborns. Testing parental samples contributed to the interpretation and reporting of results in 13/159 (8%) newborns. Our results suggest that nGS can effectively detect risk and carrier status for a wide range of disorders that are not detectable by current newborn screening assays or predicted based on the infant’s known clinical or family history, and the interpretation of results can substantially benefit from parental testing. Introduction nGS can reveal carrier-status information that could help in future reproductive planning at a time when families Recent advances in genomic sequencing (GS) technologies are having children. In addition to its utility in the have raised the possibility of its routine implementation in newborn period, nGS can provide a genomic dataset that newborn care.1,2 Newborn GS (nGS) provides many poten- can be reanalyzed throughout the individual’s life when- tial opportunities in the clinical management of a ever new indications arise. All of these potential benefits newborn. First, it might identify risk for a broad range of can be achieved with a single test, which also provides disorders in babies who are asymptomatic at birth and the opportunity to inexpensively and conveniently re- thereby expand the spectrum of conditions for which interrogate the sequence over time as needed when new screening is possible. This would avoid constraints, such healthcare issues arise. as the availability of a biochemical screening method, or Despite its anticipated benefits, some of the major chal- confounding factors, such as the baby’s gestational age at lenges in the use of nGS are the analysis, interpretation, birth, transfusion status, age at sample collection, or meta- and appropriate reporting of healthcare-related informa- bolic and feeding states. Second, nGS could reduce the tion from genomic data in a timely manner. Variant inter- diagnostic odyssey for ill newborns by allowing for the pretation, as well as the prediction of likelihood, severity, timely application of appropriate treatments. The success and timing of a phenotype from a specific variant, are of nGS in providing a rapid diagnosis for critically ill new- especially difficult in the newborn population because of borns suspected of having single-gene disorders has been the absence or obscurity of a phenotype for many disor- demonstrated in recent studies.3,4 Third, pharmacogenom- ders at birth. Yet estimating the penetrance and age-of- ics (PGx) information from nGS has the potential to onset of variants is particularly critical for newborns inform the selection and dosing of drugs for optimal treat- because of concerns about returning low-risk or adult- ment strategies in childhood and throughout life. Finally, onset findings. Predicting the inheritance pattern of 1Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; 2Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA 02139, USA; 3Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA; 4Harvard Med- ical School, Boston, MA 02115, USA; 5Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA 02115, USA; 6Department of Neurology, Boston Children’s Hospital, Boston, MA 02115, USA; 7Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; 8Division of Newborn Medicine, Boston Children’s Hospital, Boston, MA 02115, USA; 9Depart- ment of Pediatric Newborn Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; 10Center for Medical Ethics and Health Policy, Baylor Col- lege of Medicine, Houston, TX 77030, USA; 11The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; 12Center for Genomic Medicine, Mas- sachusetts General Hospital, Boston, MA 02114, USA *Correspondence: [email protected] https://doi.org/10.1016/j.ajhg.2018.11.016. Ó 2018 American Society of Human Genetics. 76 The American Journal of Human Genetics 104, 76–93, January 3, 2019 variants might not always be straightforward either fant; if applicable, consent was obtained from any non-biological because both dominant and recessive variants have been legal guardians. reported for many genes. Data derived from studies ad- dressing the technical and interpretive aspects of nGS are needed if researchers are to develop best practices for nGS Analysis its responsible and effective implementation. Newborn Whole-exome sequencing (WES) was performed at the CLIA-ac- credited Clinical Research Sequencing Platform of the Broad Sequencing in Genomic Medicine and Public Health Institute, and Sanger confirmation was performed at the CLIA- (NSIGHT) is an NIH-funded consortium of four research 5 accredited Partners Healthcare Laboratory for Molecular Medicine programs designed to address some of these questions. as previously described.8 Variants were assessed and classified as Within NSIGHT, the BabySeq Project is a pilot random- described.9,10 All nGS results were returned in a Newborn Genomic ized clinical trial that explores the application of nGS in Sequencing Report (NGSR), which included an indication-based healthy and ill newborns without selecting for those sus- analysis (IBA) for any additional diagnostic assessment related to pected to have a genetic disorder, and it assesses the med- a clinical indication. The first page of the NGSRs summarized the ical, behavioral, and economic impacts of nGS.6 Here we analysis approach and the results in order to concisely communi- present the analysis and reporting of nGS results in 159 cate key findings from the nGS; subsequent pages provided more newborns enrolled in the BabySeq Project; the report in- detailed information about each reported variant; such informa- cludes (1) risk and carrier status for childhood-onset dis- tion included gene coverage, interpretation of the variant’s clinical significance, a summary of related disease(s), and associated repro- ease, (2) risk for medically actionable adult-onset disease, ductive risks. The criteria used for return of results were as previ- (3) selected PGx findings relevant to medications used in ously described.6 In brief, three groups of results were returned in pediatrics, and (4) variants related to a specific indication the NGSR: (1) monogenic disease risks (MDR, defined as pathogenic that either was present at birth or arose during the course or likely pathogenic [P/LP] variants in genes associated with domi- of the study. nantly inherited diseases or as bi-allelic P/LP variants in genes asso- ciated with recessively inherited diseases) that present or are manageable during childhood (i.e., the earliest reported onset is Subjects and Methods before the age of 18); (2) carrier status for any gene meeting the MDR reporting criteria; and (3) PGx-associated genes, which were The BabySeq Project Study Design captured by our WES method, that are related to atypical reactions A description of the BabySeq Project, the enrollment process, and to medications used in the pediatric population. Later in the study, the demographic characteristics of the participants has been pub- information about risk for a limited number of actionable adult- lished elsewhere.6,7 In brief, two cohorts of newborns and their onset conditions (for which screening, treatment, and preventative parents were enrolled in the BabySeq Project: (1) healthy new- actions that would significantly reduce morbidity and mortality are borns from the well-baby nursery at Brigham and Women’s Hospi- available during adulthood) was also offered for return, and this tal (BWH) and (2) ill newborns from the neonatal and pediatric information was included in the NGSRs for newborns whose par- intensive care units (NICUs) at Boston Children’s Hospital ents consented to receive this information for their infant. The (BCH), BWH, and Massachusetts General Hospital (MGH). Enroll- actionable adult-onset disease-associated genes included five addi- ees from the NICUs were not preselected on the basis of having a tional genes (BRCA1 [MIM: 113705], BRCA2 [MIM: 600185], MLH1 suspected genetic disorder. Three-generation pedigrees were ob- [MIM: 120436], MSH2 [MIM: 609309], and MSH6 [MIM: 600678]), tained for each family during the consent and enrollment sessions which are all found on ACMG 59, a list of clinically important genes with a genetic counselor.