A recurrent 16p12.1 microdeletion supports a two-hit model for severe developmental delay
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We report the identification of a recurrent, 520-kb 16p12.1 microdeletion associated with childhood developmental delay. The microdeletion was detected in 20 of 11,873 cases compared with 2 of 8,540 controls (P = 0.0009, OR = 7.2) and replicated in a second series of 22 of 9,254 cases compared with 6 of 6,299 controls (P = 0.028, OR = 2.5). Most deletions were inherited, with carrier parents likely to manifest neuropsychiatric phenotypes compared to non-carrier parents (P = 0.037, OR = 6). Probands were more likely to carry an additional large copy-number variant when compared to matched controls (10 of 42 cases, P = 5.7 x 10(-5), OR = 6.6). The clinical features of individuals with two mutations were distinct from and/or more severe than those of individuals carrying only the co-occurring mutation. Our data support a two-hit model in which the 16p12.1 microdeletion both predisposes to neuropsychiatric phenotypes as a single event and exacerbates neurodevelopmental phenotypes in association with other large deletions or duplications. Analysis of other microdeletions with variable expressivity indicates that this two-hit model might be more generally applicable to neuropsychiatric disease.
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Low penetrance estimates may relate to subclinical manifestations of neuropsychiatric or behavioral problems or incomplete information about the parents of individuals with the 15q11.2 BP1-BP2 microdeletion or members of control cohorts.
“Low penetrance estimates may relate to subclinical manifestations of neuropsychiatric/behavioral problems or incomplete information about the parents of individuals with 15q11.2 BP1–BP2 microdeletion or members of control cohorts [44].”
From The 15q11.2 BP1–BP2 Microdeletion Syndrome: A Review (2015) · cites this paper as [44]
The Discussion (page unavailable) says subtle features of the 16p12.1 microdeletion may lead to under-ascertainment, and it reports neuropsychiatric features in carrier parents. It does not establish this explanation for low penetrance estimates of the distinct 15q11.2 BP1–BP2 microdeletion or attribute those estimates to incomplete information about parents or control cohorts. (LLM, conf=0.79)
Experimental — accuracy not yet measuredFor a 500 kb deletion of 16p12.1, carriers with developmental delay had an increased burden of secondary CNVs compared to controls.
“Deletion carriers with developmental delay had an increased burden of secondary CNVs compared to deletion carriers in controls.”
From Getting to the cores of autism (2019) · cites this paper as Girirajan et al., 2010
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- Authors
- Girirajan, S., Rosenfeld, J. A., Cooper, G. M., Antonacci, F., Siswara, P., Itsara, A., Vives, L., Walsh, T., McCarthy, S. E., Baker, C., Mefford, H. C., Kidd, J. M., Browning, S. R., Browning, B. L., Dickel, D. E., Levy, D. L., Ballif, B. C., Platky, K., Farber, D. M., Gowans, G. C., Wetherbee, J. J., Asamoah, A., Weaver, D. D., Mark, P. R., Dickerson, J., Garg, B. P., Ellingwood, S. A., Smith, R., Banks, V. C., Smith, W., McDonald, M. T., Hoo, J. J., French, B. N., Hudson, C., Johnson, J. P., Ozmore, J. R., Moeschler, J. B., Surti, U., Escobar, L. F., El-Khechen, D., Gorski, J. L., Kussmann, J., Salbert, B., Lacassie, Y., Biser, A., McDonald-McGinn, D. M., Zackai, E. H., Deardorff, M. A., Shaikh, T. H., Haan, E., Friend, K. L., Fichera, M., Romano, C., Gécz, J., DeLisi, L. E., Sebat, J., King, M.-C., Shaffer, L. G., & Eichler, E. E.
- Affiliations
- University of Washington (US)
- Cold Spring Harbor Laboratory (US)
- University of Auckland (NZ)
- Harvard University (US)
- University of Louisville (US)
- Indiana University Indianapolis (US)
- Maine Medical Center (US)
- Duke Medical Center (US)
- University of Toledo Medical Center (US)
- Shodair Children's Hospital (US)
- Dartmouth–Hitchcock Medical Center (US)
- Magee-Womens Hospital (US)
- St Vincent Hospital (US)
- University of Missouri (US)
- Geisinger Medical Center (US)
- Louisiana State University (US)
- Children's Hospital of Philadelphia (US)
- South Australia Pathology (AU)
- Oasi Maria SS (IT)
- University of California San Diego (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Eichler, Evan E
- ORCID
- Girirajan, Santhosh
- Rosenfeld, Jill A
- Cooper, Gregory M
- Antonacci, Francesca
- Walsh, Tom
- Mefford, Heather C
- Kidd, Jeffrey M
- Browning, Sharon R
- Browning, Brian L
- Dickel, Diane E
- Levy, Deborah L
- Weaver, David D
- Mark, Paul R
- Smith, Wendy
- McDonald, Marie T
- Surti, Urvashi
- Escobar, Luis F
- Lacassie, Yves
- Zackai, Elaine H
- Deardorff, Matthew A
- Shaikh, Tamim H
- Haan, Eric
- Friend, Kathryn L
- Fichera, Marco
- Romano, Corrado
- Gécz, Jozef
- DeLisi, Lynn E
- Sebat, Jonathan
- King, Mary-Claire
- Shaffer, Lisa G
- Eichler, Evan E
- Venue
- Nature Genetics
- Published
- 2010-02-14
- Volume
- 42
- Issue
- 3
- Pages
- 203-209
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC2847896
- OpenAlex
- W2137289649
- Cited by
- 667
- References
- 50
- Citations by year
- 2026: 8 · 2025: 15 · 2024: 19 · 2023: 12 · 2022: 25 · 2021: 28 · 2020: 28 · 2019: 19 · 2018: 61 · 2017: 28 · 2016: 36 · 2015: 52 · 2014: 45 · 2013: 67 · 2012: 74
- FWCI
- 52.11
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
- Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- CINECA IRIS Institutional Research Information System (University of Bari Aldo Moro) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- U.S. Department of Health and Human Services
- National Institutes of Health
- National Institute on Aging
- National Institute of General Medical Sciences (T32GM007266)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (HD065285, R01HD065285)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Keywords
- two-hit model, developmental delay, neuropsychiatric phenotypes, copy number variation, variable expressivity, microdeletion syndromes, neurodevelopmental disorders, genotype-phenotype correlation
- MeSH terms
- Adult, Child, Developmental Disabilities, Child, Preschool, Chromosome Deletion, Chromosomes, Human, Pair 16, Family, Gene Frequency, Humans, Infant, Models, Genetic, Pedigree, Phenotype, Recurrence, Severity of Illness Index, Case-Control Studies, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Comparative Genomic Hybridization
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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