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Article ; Online: Privacy Risks in Prenatal Aneuploidy and Carrier Screening: What Obstetricians and Their Patients Need to Know.

Parobek, Christian M / Russo, Melissa L / Lewkowitz, Adam K

2021 Volume 137, Issue 6, Page(s) 1074–1079

Abstract: Modern prenatal genetic screening techniques such as cell-free fetal DNA and expanded carrier screening genotype substantial amounts of maternal and fetoplacental DNA. Although DNA can be deidentified by stripping protected health information from ... ...

Abstract	Modern prenatal genetic screening techniques such as cell-free fetal DNA and expanded carrier screening genotype substantial amounts of maternal and fetoplacental DNA. Although DNA can be deidentified by stripping protected health information from genetic data, anonymized DNA can be reidentified using genetic databases, raising long-term genetic privacy concerns for both mother and fetus. In this commentary, we explore the evolution of prenatal genetic screening and how modern screening techniques may pose unanticipated privacy risks. We highlight knowledge gaps and outline steps to improve patient awareness of and control over their genetic privacy, including specific recommendations for laboratories and prenatal care practitioners who offer screening. We also encourage our colleagues who provide prenatal care to be well informed about the privacy implications of the genetic tests we order and to be vocal advocates for our patients' genetic privacy, both with the laboratories that perform these tests and in the public sphere.
MeSH term(s)	Aneuploidy ; Cell-Free Nucleic Acids/analysis ; Databases, Genetic ; Female ; Genetic Carrier Screening/ethics ; Genetic Privacy ; Humans ; Information Dissemination ; Information Storage and Retrieval ; Laboratories/organization & administration ; Obstetrics ; Patient Education as Topic ; Pregnancy ; Prenatal Diagnosis ; Risk Factors
Chemical Substances	Cell-Free Nucleic Acids
Language	English
Publishing date	2021-05-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	207330-4
ISSN	1873-233X ; 0029-7844
ISSN (online)	1873-233X
ISSN	0029-7844
DOI	10.1097/AOG.0000000000004387
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Article ; Online: Inconsistent use of alpha-fetoprotein as a screen for fetal anomalies.

Parobek, Christian M / Has, Phinnara / Lorenzi, Paula / Clark, Melissa A / Lewkowitz, Adam K / Russo, Melissa L

American journal of obstetrics & gynecology MFM

2023 Volume 5, Issue 10, Page(s) 101133

Language	English
Publishing date	2023-08-16
Publishing country	United States
Document type	Letter
ISSN	2589-9333
ISSN (online)	2589-9333
DOI	10.1016/j.ajogmf.2023.101133
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Article ; Online: Privacy practices using genetic data from cell-free DNA aneuploidy screening.

Parobek, Christian M / Russo, Melissa L / Lewkowitz, Adam K

Genetics in medicine : official journal of the American College of Medical Genetics

2021 Volume 23, Issue 9, Page(s) 1746–1752

Abstract: Purpose: Cell-free fetal DNA (cfDNA) analyzes maternal and fetoplacental DNA, generating highly personal genetic information for both mother and fetus. This study aimed to determine how laboratories retain, use, and share genetic information from cfDNA. ...

Abstract	Purpose: Cell-free fetal DNA (cfDNA) analyzes maternal and fetoplacental DNA, generating highly personal genetic information for both mother and fetus. This study aimed to determine how laboratories retain, use, and share genetic information from cfDNA. Other outcomes included laboratories' adherence to American Society of Human Genetics (ASHG) privacy principles, and the readability of privacy policies. Methods: Laboratories offering cfDNA aneuploidy screening were identified from online searches, curated databases, and a genomics news website. Of 124 laboratories identified, 13 were commercial laboratories offering cfDNA aneuploidy screening in the United States, and were included. Genetic privacy policies from eligible laboratories were identified by reviewing requisition and consent forms, which were obtained online or by direct contact. Results: Most laboratories use prenatal genetic information for research (n = 10, 77%), and more than half (n = 7, 54%) shared genetic information with others. Overall, laboratories inadequately disclosed privacy risks. In a readability analysis, 9 of 11 (82%) laboratories' genetic privacy policies were written at or above a 12th grade reading level. Conclusion: Most laboratories allowed for prolonged use and sharing of cfDNA data, demonstrated incomplete adherence to ASHG privacy recommendations, and provided consents written in college-level language. Laboratories should revise their consent forms, and providers should help patients understand these forms.
MeSH term(s)	Aneuploidy ; Cell-Free Nucleic Acids/genetics ; Female ; Genetic Privacy ; Genetic Testing ; Humans ; Pregnancy ; Prenatal Diagnosis ; Privacy ; United States
Chemical Substances	Cell-Free Nucleic Acids
Language	English
Publishing date	2021-05-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1455352-1
ISSN	1530-0366 ; 1098-3600
ISSN (online)	1530-0366
ISSN	1098-3600
DOI	10.1038/s41436-021-01205-x
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Article ; Online: Clinical exome sequencing uncovers genetic disorders in neonates with suspected hypoxic-ischemic encephalopathy: A retrospective analysis.

Parobek, Christian M / Zemet, Roni / Shanahan, Matthew A / Burnett, Brian A / Mizerik, Elizabeth / Rosenfeld, Jill A / Vossaert, Liesbeth / Clark, Steven L / Hunter, Jill V / Lalani, Seema R

Clinical genetics

2024

Abstract: Hypoxic-ischemic encephalopathy (HIE) occurs in up to 7 out of 1000 births and accounts for almost a quarter of neonatal deaths worldwide. Despite the name, many newborns with HIE have little evidence of perinatal hypoxia. We hypothesized that some ... ...

Abstract	Hypoxic-ischemic encephalopathy (HIE) occurs in up to 7 out of 1000 births and accounts for almost a quarter of neonatal deaths worldwide. Despite the name, many newborns with HIE have little evidence of perinatal hypoxia. We hypothesized that some infants with HIE have genetic disorders that resemble encephalopathy. We reviewed genetic results for newborns with HIE undergoing exome or genome sequencing at a clinical laboratory (2014-2022). Neonates were included if they had a diagnosis of HIE and were delivered ≥35 weeks. Neonates were excluded for cardiopulmonary pathology resulting in hypoxemia or if neuroimaging suggested postnatal hypoxic-ischemic injury. Of 24 patients meeting inclusion criteria, six (25%) were diagnosed with a genetic condition. Four neonates had variants at loci linked to conditions with phenotypic features resembling HIE, including KIF1A, GBE1, ACTA1, and a 15q13.3 deletion. Two additional neonates had variants in genes not previously associated with encephalopathy, including DUOX2 and PTPN11. Of the six neonates with a molecular diagnosis, two had isolated HIE without apparent comorbidities to suggest a genetic disorder. Genetic diagnoses were identified among neonates with and without sentinel labor events, abnormal umbilical cord gasses, and low Apgar scores. These results suggest that genetic evaluation is clinically relevant for patients with perinatal HIE.
Language	English
Publishing date	2024-03-28
Publishing country	Denmark
Document type	Journal Article
ZDB-ID	221209-2
ISSN	1399-0004 ; 0009-9163
ISSN (online)	1399-0004
ISSN	0009-9163
DOI	10.1111/cge.14522
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Article ; Online: What test did I have? Patient uncertainty about prenatal genetic screening.

Parobek, Christian M / Has, Phinnara / Lorenzi, Paula / Russo, Melissa L / Clark, Melissa A / Lewkowitz, Adam K

American journal of obstetrics and gynecology

2021 Volume 225, Issue 3, Page(s) 341–342

MeSH term(s)	Adult ; Age Factors ; Awareness ; Female ; Genetic Carrier Screening ; Humans ; Pregnancy ; Prenatal Diagnosis ; Risk Assessment ; Surveys and Questionnaires ; Uncertainty
Language	English
Publishing date	2021-05-27
Publishing country	United States
Document type	Letter ; Randomized Controlled Trial ; Research Support, Non-U.S. Gov't
ZDB-ID	80016-8
ISSN	1097-6868 ; 0002-9378
ISSN (online)	1097-6868
ISSN	0002-9378
DOI	10.1016/j.ajog.2021.05.030
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Article ; Online: Video education about genetic privacy and patient perspectives about sharing prenatal genetic data: a randomized trial.

Parobek, Christian M / Thorsen, Margaret M / Has, Phinnara / Lorenzi, Paula / Clark, Melissa A / Russo, Melissa L / Lewkowitz, Adam K

American journal of obstetrics and gynecology

2022 Volume 227, Issue 1, Page(s) 87.e1–87.e13

Abstract: Background: Laboratories offering cell-free DNA often reserve the right to share prenatal genetic data for research or even commercial purposes, and obtain this permission on the patient consent form. Although it is known that nonpregnant patients are ... ...

Abstract	Background: Laboratories offering cell-free DNA often reserve the right to share prenatal genetic data for research or even commercial purposes, and obtain this permission on the patient consent form. Although it is known that nonpregnant patients are often reluctant to share their genetic data for research, pregnant patients' knowledge of, and opinions about, genetic data privacy are unknown. Objective: We investigated whether pregnant patients who had already undergone cell-free DNA screening were aware that genetic data derived from cell-free DNA may be shared for research. Furthermore, we examined whether pregnant patients exposed to video education about the Genetic Information Nondiscrimination Act-a federal law that mandates workplace and health insurance protections against genetic discrimination-were more willing to share cell-free DNA-related genetic data for research than pregnant patients who were unexposed. Study design: In this randomized controlled trial (ClinicalTrials.gov Identifier: NCT04420858), English-speaking patients with singleton pregnancies who underwent cell-free DNA and subsequently presented at 17 0/7 to 23 6/7 weeks of gestation for a detailed anatomy scan were randomized 1:1 to a control or intervention group. Both groups viewed an infographic about cell-free DNA. In addition, the intervention group viewed an educational video about the Genetic Information Nondiscrimination Act. The primary outcomes were knowledge about, and willingness to share, prenatal genetic data from cell-free DNA by commercial laboratories for nonclinical purposes, such as research. The secondary outcomes included knowledge about existing genetic privacy laws, knowledge about the potential for reidentification of anonymized genetic data, and acceptability of various use and sharing scenarios for prenatal genetic data. Eighty-one participants per group were required for 80% power to detect an increase in willingness to share data from 60% to 80% (α=0.05). Results: A total of 747 pregnant patients were screened, and 213 patients were deemed eligible and approached for potential study participation. Of these patients, 163 (76.5%) consented and were randomized; one participant discontinued the intervention, and two participants were excluded from analysis after the intervention when it was discovered that they did not fulfill all eligibility criteria. Overall, 160 (75.1%) of those approached were included in the final analysis. Most patients in the control group (72 [90.0%]) and intervention (76 [97.4%]) group were either unsure about or incorrectly thought that cell-free DNA companies could not share prenatal genetic data for research. Participants in the intervention group were more likely to incorrectly believe that their prenatal genetic data would not be shared for nonclinical purposes than participants in the control group (28.8% in the control group vs 46.2% in the intervention; P=.03). However, video education did not increase participant willingness to share genetic data in multiple scenarios. Non-White participants were less willing than White participants to allow sharing of genetic data specifically for academic research (P<.001). Conclusion: Most participants were unaware that their prenatal genetic data may be used for nonclinical purposes. Pregnant patients who were educated about the Genetic Information Nondiscrimination Act were not more willing to share genetic data than those who did not receive this education. Surprisingly, video education about the Genetic Information Nondiscrimination Act led patients to falsely believe that their data would not be shared for research, and participants who identified as racial minorities were less willing to share genetic data. New strategies are needed to improve pregnant patients' understanding of genetic privacy.
MeSH term(s)	Audiovisual Aids ; Cell-Free Nucleic Acids ; Female ; Genetic Privacy ; Humans ; Patient Education as Topic ; Pregnancy
Chemical Substances	Cell-Free Nucleic Acids
Language	English
Publishing date	2022-03-26
Publishing country	United States
Document type	Journal Article ; Randomized Controlled Trial
ZDB-ID	80016-8
ISSN	1097-6868 ; 0002-9378
ISSN (online)	1097-6868
ISSN	0002-9378
DOI	10.1016/j.ajog.2022.03.047
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Article ; Online: SeekDeep: single-base resolution de novo clustering for amplicon deep sequencing.

Hathaway, Nicholas J / Parobek, Christian M / Juliano, Jonathan J / Bailey, Jeffrey A

Nucleic acids research

2017 Volume 46, Issue 4, Page(s) e21

Abstract: PCR amplicon deep sequencing continues to transform the investigation of genetic diversity in viral, bacterial, and eukaryotic populations. In eukaryotic populations such as Plasmodium falciparum infections, it is important to discriminate sequences ... ...

Abstract	PCR amplicon deep sequencing continues to transform the investigation of genetic diversity in viral, bacterial, and eukaryotic populations. In eukaryotic populations such as Plasmodium falciparum infections, it is important to discriminate sequences differing by a single nucleotide polymorphism. In bacterial populations, single-base resolution can provide improved resolution towards species and strains. Here, we introduce the SeekDeep suite built around the qluster algorithm, which is capable of accurately building de novo clusters representing true, biological local haplotypes differing by just a single base. It outperforms current software, particularly at low frequencies and at low input read depths, whether resolving single-base differences or traditional OTUs. SeekDeep is open source and works with all major sequencing technologies, making it broadly useful in a wide variety of applications of amplicon deep sequencing to extract accurate and maximal biologic information.
MeSH term(s)	Cluster Analysis ; Haplotypes ; High-Throughput Nucleotide Sequencing/methods ; Microbiota/genetics ; Plasmodium falciparum/genetics ; Polymorphism, Single Nucleotide ; Software
Language	English
Publishing date	2017-11-16
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkx1201
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Article ; Online: Haemoglobinopathies and the clinical epidemiology of malaria: a systematic review and meta-analysis.

Taylor, Steve M / Parobek, Christian M / Fairhurst, Rick M

The Lancet. Infectious diseases

2012 Volume 12, Issue 6, Page(s) 457–468

Abstract: Background: Haemoglobinopathies can reduce the risk of malaria syndromes. We aimed to quantify the relation between different haemoglobin mutations and malaria protection to strengthen the foundation for translational studies of malaria pathogenesis and ...

Abstract	Background: Haemoglobinopathies can reduce the risk of malaria syndromes. We aimed to quantify the relation between different haemoglobin mutations and malaria protection to strengthen the foundation for translational studies of malaria pathogenesis and immunity. Methods: We systematically searched the Medline and Embase databases for studies that estimated the risk of malaria in patients with and without haemoglobinopathies up to Sept 9, 2011, and identified additional studies from reference lists. We included studies that enrolled mainly children or pregnant women and had the following outcomes: Plasmodium falciparum severe malaria, uncomplicated malaria, asymptomatic parasitaemia, or pregnancy-associated malaria, and Plasmodium vivax malaria. Two reviewers identified studies independently, assessed quality of the studies, and extracted data. We produced odds ratios (ORs; 95% CIs) for case-control studies and incidence rate ratios (IRRs; 95% CIs) for prospective studies. We did the meta-analysis with a random-effects model when equivalent outcomes were reported in more than one study. Findings: Of 62 identified studies, 44 reported data for haemoglobin AS, 19 for haemoglobin AC and CC, and 18 for α-thalassaemia. Meta-analysis of case-control studies showed a decreased risk of severe P. falciparum malaria in individuals with haemoglobin AS (OR 0·09, 95% CI 0·06-0·12), haemoglobin CC (0·27, 0·11-0·63), haemoglobin AC (0·83, 0·67-0·96), homozygous α-thalassaemia (0·63, 0·48-0·83), and heterozygous α-thalassaemia (0·83, 0·74-0·92). In meta-analysis of prospective trials only haemoglobin AS was consistently associated with protection from uncomplicated malaria (IRR 0·69, 95% CI 0·61-0·79); no haemoglobinopathies led to consistent protection from asymptomatic parasitaemia. Few clinical studies have investigated β-thalassaemia, haemoglobin E, P. vivax malaria, or pregnancy-associated malaria. Interpretation: Haemoglobin AS, CC, and AC genotypes and homozygous and heterozygous α-thalassaemia provide significant protection from severe malaria syndromes, but these haemoglobinopathies differ substantially in the degree of protection provided and confer mild or no protection against uncomplicated malaria and asymptomatic parasitaemia. Through attenuation of severity of malaria, haemoglobinopathies could serve as a model for investigation of the mechanisms of malaria pathogenesis and immunity. Funding: US National Institute of Allergy and Infectious Diseases.
MeSH term(s)	Hemoglobin, Sickle ; Hemoglobinopathies/blood ; Hemoglobinopathies/genetics ; Humans ; Malaria/blood ; Malaria/epidemiology ; Malaria/prevention & control ; Malaria, Falciparum/epidemiology ; Risk Factors ; alpha-Thalassemia/blood
Chemical Substances	Hemoglobin, Sickle ; hemoglobin AS (52012-19-8)
Language	English
Publishing date	2012-03-23
Publishing country	United States
Document type	Journal Article ; Meta-Analysis ; Research Support, N.I.H., Intramural ; Review ; Systematic Review
ZDB-ID	2061641-7
ISSN	1474-4457 ; 1473-3099
ISSN (online)	1474-4457
ISSN	1473-3099
DOI	10.1016/S1473-3099(12)70055-5
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Article ; Online: A Prolonged Outbreak of KPC-3-Producing Enterobacter cloacae and Klebsiella pneumoniae Driven by Multiple Mechanisms of Resistance Transmission at a Large Academic Burn Center.

Kanamori, Hajime / Parobek, Christian M / Juliano, Jonathan J / van Duin, David / Cairns, Bruce A / Weber, David J / Rutala, William A

Antimicrobial agents and chemotherapy

2017 Volume 61, Issue 2

Abstract: Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacter cloacae has been recently recognized in the United States. Whole-genome sequencing (WGS) has become a useful tool for analysis of outbreaks and for determining transmission networks of ... ...

Abstract	Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacter cloacae has been recently recognized in the United States. Whole-genome sequencing (WGS) has become a useful tool for analysis of outbreaks and for determining transmission networks of multidrug-resistant organisms in health care settings, including carbapenem-resistant Enterobacteriaceae (CRE). We experienced a prolonged outbreak of CRE E. cloacae and K. pneumoniae over a 3-year period at a large academic burn center despite rigorous infection control measures. To understand the molecular mechanisms that sustained this outbreak, we investigated the CRE outbreak isolates by using WGS. Twenty-two clinical isolates of CRE, including E. cloacae (n = 15) and K. pneumoniae (n = 7), were sequenced and analyzed genetically. WGS revealed that this outbreak, which seemed epidemiologically unlinked, was in fact genetically linked over a prolonged period. Multiple mechanisms were found to account for the ongoing outbreak of KPC-3-producing E. cloacae and K. pneumoniae This outbreak was primarily maintained by a clonal expansion of E. cloacae sequence type 114 (ST114) with distribution of multiple resistance determinants. Plasmid and transposon analyses suggested that the majority of bla
MeSH term(s)	Adult ; Aged ; Bacterial Proteins/genetics ; Burn Units ; Disease Outbreaks ; Drug Resistance, Multiple, Bacterial/drug effects ; Drug Resistance, Multiple, Bacterial/genetics ; Enterobacter cloacae/drug effects ; Enterobacter cloacae/genetics ; Enterobacter cloacae/pathogenicity ; Enterobacteriaceae Infections/drug therapy ; Enterobacteriaceae Infections/epidemiology ; Enterobacteriaceae Infections/microbiology ; Female ; Genome, Bacterial ; Humans ; Klebsiella Infections/drug therapy ; Klebsiella Infections/epidemiology ; Klebsiella Infections/microbiology ; Klebsiella pneumoniae/drug effects ; Klebsiella pneumoniae/genetics ; Klebsiella pneumoniae/pathogenicity ; Male ; Microbial Sensitivity Tests ; Middle Aged ; North Carolina/epidemiology ; beta-Lactamases/genetics
Chemical Substances	Bacterial Proteins ; beta-Lactamases (EC 3.5.2.6) ; beta-lactamase KPC-3, Enterobacter cloacae (EC 3.5.2.6) ; beta-lactamase KPC-3, Klebsiella pneumoniae (EC 3.5.2.6)
Language	English
Publishing date	2017-01-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	217602-6
ISSN	1098-6596 ; 0066-4804
ISSN (online)	1098-6596
ISSN	0066-4804
DOI	10.1128/AAC.01516-16
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Article: skelesim: an extensible, general framework for population genetic simulation in R

Parobek, Christian M / Allan E. Strand / Frederick I. Archer / Libby Liggins / Michelle E. DePrengerâLevin / Sean M. Hoban

Molecular ecology resources. 2017 Jan., v. 17, no. 1

2017

Abstract: Simulations are a key tool in molecular ecology for inference and forecasting, as well as for evaluating new methods. Due to growing computational power and a diversity of software with different capabilities, simulations are becoming increasingly ... ...

Abstract	Simulations are a key tool in molecular ecology for inference and forecasting, as well as for evaluating new methods. Due to growing computational power and a diversity of software with different capabilities, simulations are becoming increasingly powerful and useful. However, the widespread use of simulations by geneticists and ecologists is hindered by difficulties in understanding these softwares' complex capabilities, composing code and input files, a daunting bioinformatics barrier and a steep conceptual learning curve. skelesim (an R package) guides users in choosing appropriate simulations, setting parameters, calculating genetic summary statistics and organizing data output, in a reproducible pipeline within the R environment. skelesim is designed to be an extensible framework that can âwrapâ around any simulation software (inside or outside the R environment) and be extended to calculate and graph any genetic summary statistics. Currently, skelesim implements coalescent and forwardâtime models available in the fastsimcoal2 and rmetasim simulation engines to produce null distributions for multiple population genetic statistics and marker types, under a variety of demographic conditions. skelesim is intended to make simulations easier while still allowing full model complexity to ensure that simulations play a fundamental role in molecular ecology investigations. skelesim can also serve as a teaching tool: demonstrating the outcomes of stochastic population genetic processes; teaching general concepts of simulations; and providing an introduction to the R environment with a userâfriendly graphical user interface (using shiny).
Keywords	bioinformatics ; computer software ; ecology ; geneticists ; models ; statistics ; user interface
Language	English
Dates of publication	2017-01
Size	p. 101-109.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2406816-0
ISSN	1471-8286 ; 1755-098X
ISSN (online)	1471-8286
ISSN	1755-098X
DOI	10.1111/1755-0998.12607
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