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| Content Provider | World Health Organization (WHO)-Global Index Medicus |
|---|---|
| Author | Jensen, Taylor J. Kim, Sung K. Van Den Boom, Dirk Deciu, Cosmin Ehrich, Mathias |
| Description | Author Affiliation: Jensen TJ ( Sequenom Laboratories, San Diego, CA); Kim SK ( Sequenom Laboratories, San Diego, CA); van den Boom D ( Sequenom Inc., San Diego, CA.); Deciu C ( Sequenom Laboratories, San Diego, CA); Ehrich M ( Sequenom Inc., San Diego, CA. mehrich@sequenom.com.) |
| Abstract | BACKGROUND: Massively parallel sequencing of circulating cell free (ccf) DNA from maternal plasma has been demonstrated to be a powerful method for the detection of fetal copy number variations (CNVs). Although the detection of CNVs has been described by multiple independent groups, genomic aberrations resulting in copy number-neutral events including balanced translocations have proven to be more challenging to detect noninvasively from ccf DNA. METHODS: Data modeling was initially performed to evaluate multiple methods, ultimately leveraging the short length of ccf DNA and paired-end sequencing to construct read-specific mapping characteristics. After testing in a model system, we evaluated the methods on ccf DNA isolated from the plasma of a donor known to be carrying a fetus with a balanced translocation [t(8;11)]. Sequencing was performed with Illumina sequencing technology. RESULTS: Our methodology identified the known translocation (P = 1.21 × 10(-8)) and discounted the likelihood of others, enabling the base specific identification of the rearrangement positions. In total, 402 unique sequencing reads spanned the putative breakpoints, of which 76 contained the structural rearrangement. In addition, 38 of the chimeric reads were mapped to each of the resulting derivative chromosomes, supporting the presence of a reciprocal translocation. Finally, we identified a 6-bp deletion present within der(8) that was absent from the der(11) reciprocal rearrangement. CONCLUSIONS: We have developed an algorithm to detect balanced rearrangements and applied our methodology to demonstrate the first proof-of-principle study on the noninvasive detection of a fetal-specific balanced translocation by sequencing ccf DNA from maternal plasma. |
| File Format | HTM / HTML |
| ISSN | 00099147 |
| e-ISSN | 15308561 |
| Journal | Clinical Chemistry |
| Issue Number | 10 |
| Volume Number | 60 |
| Language | English |
| Publisher | American Association for Clinical Chemistry |
| Publisher Date | 2014-10-01 |
| Publisher Place | United States |
| Access Restriction | Open |
| Subject Keyword | Dna Copy Number Variations Translocation, Genetic Molecular Sequence Data Discipline Laboratory Medicine Blood Computer Simulation Genetics Fetus High-throughput Nucleotide Sequencing Prenatal Diagnosis Chromosomes, Human, Pair 8 Metabolism Gestational Age Sequence Analysis, Dna Pregnancy Discipline Clinical Chemistry Algorithms Chromosomes, Human, Pair 11 Models, Genetic |
| Content Type | Text |
| Resource Type | Article |
| Subject | Biochemistry (medical) Clinical Biochemistry |
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