Evidence map›Paper›PMID 23695279›Full record

ArticleEuropean journal of human genetics : EJHG2014

Combined array CGH plus SNP genome analyses in a single assay for optimized clinical testing.

Joanna Wiszniewska, Weimin Bi, Chad Shaw, Pawel Stankiewicz, Sung-Hae L Kang, Amber N Pursley, Seema Lalani, Patricia Hixson, Tomasz Gambin, Chun-hui Tsai and 10 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in European journal of human genetics : EJHG, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 papers.

0numbers the graph read from it
0cells of the map it votes in
80citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

80 citing papers in PubMed.

  1. Clinical performance of the CytoScan Dx Assay in diagnosing developmental delay/intellectual disability.Genetics in medicine : official journal of the American College of Medical Genetics · 2016
    Trial
  2. Trial
  3. Article
  4. Article
  5. Review
  6. Review
  7. Article
  8. Article
  9. Article
  10. Article
  11. Article
  12. Review
  13. Article
  14. Article
  15. Review
  16. Article
  17. Article
  18. A founderFrontiers in medicine · 2023
    Article
  19. Article
  20. Review

20 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

20 authors.

Joanna WiszniewskaDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Weimin BiDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Chad ShawDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Pawel StankiewiczDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Sung-Hae L KangAllina Cytogenetics Laboratory, Abbott Northwestern Hospital, Minneapolis, MN, USA.
Amber N PursleyDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Seema Lalani1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA [2] Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
Patricia HixsonDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Tomasz GambinInstitute of Computer Science, Warsaw University of Technology, Warsaw, Poland.
Chun-hui Tsai1] Department of Molecular and Medical Genetics, Oregon Health and Sciences University-OHSU, Portland, OR, USA [2] Department of Pediatrics, The Children's Hospital, University of Colorado School of Medicine, Aurora, CO, USA.
Hans-Georg BockDepartment of Pediatrics, University of Mississippi Medical Center, Jackson, MS, USA.
Maria DescartesDepartment of Genetics, University of Alabama, Birmingham, AL, USA.
Frank J Probst1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA [2] Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
Fernando ScagliaDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Arthur L Beaudet1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA [2] Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
James R Lupski1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA [2] Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
Christine Eng1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA [2] Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
Sau Wai Cheung1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA [2] Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
Carlos Bacino1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA [2] Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
Ankita PatelDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

In clinical diagnostics, both array comparative genomic hybridization (array CGH) and single nucleotide polymorphism (SNP) genotyping have proven to be powerful genomic technologies utilized for the evaluation of developmental delay, multiple congenital anomalies, and neuropsychiatric disorders. Differences in the ability to resolve genomic changes between these arrays may constitute an implementation challenge for clinicians: which platform (SNP vs array CGH) might best detect the underlying genetic cause for the disease in the patient? While only SNP arrays enable the detection of copy number neutral regions of absence of heterozygosity (AOH), they have limited ability to detect single-exon copy number variants (CNVs) due to the distribution of SNPs across the genome. To provide comprehensive clinical testing for both CNVs and copy-neutral AOH, we enhanced our custom-designed high-resolution oligonucleotide array that has exon-targeted coverage of 1860 genes with 60,000 SNP probes, referred to as Chromosomal Microarray Analysis - Comprehensive (CMA-COMP). Of the 3240 cases evaluated by this array, clinically significant CNVs were detected in 445 cases including 21 cases with exonic events. In addition, 162 cases (5.0%) showed at least one AOH region >10 Mb. We demonstrate that even though this array has a lower density of SNP probes than other commercially available SNP arrays, it reliably detected AOH events >10 Mb as well as exonic CNVs beyond the detection limitations of SNP genotyping. Thus, combining SNP probes and exon-targeted array CGH into one platform provides clinically useful genetic screening in an efficient manner.

Indexed as

Comparative Genomic HybridizationDNA Copy Number VariationsGenome, HumanGenomicsGenotyping TechniquesHeterozygoteHumansOligonucleotide Array Sequence AnalysisPolymorphism, Single Nucleotide

Identifiers

PMID23695279
PMCPMC3865406

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.