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Normalizing chromosomes for the determination and verification of common and rare chromosomal aneuploidies

A technique for aneuploidy and chromosomes, applied in the determination/inspection of microorganisms, special data processing applications, biochemical equipment and methods, etc.

Active Publication Date: 2013-03-20
VERINATA HEALTH INC
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0004] Limitations of existing methods underlie the need for optimal non-invasive methods that will provide specificity, sensitivity for prenatal diagnosis and diagnosis and monitoring of medical conditions associated with copy number changes and suitability for any or both of these to reliably diagnose chromosomal aneuploidy

Method used

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  • Normalizing chromosomes for the determination and verification of common and rare chromosomal aneuploidies
  • Normalizing chromosomes for the determination and verification of common and rare chromosomal aneuploidies
  • Normalizing chromosomes for the determination and verification of common and rare chromosomal aneuploidies

Examples

Experimental program
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Effect test

example 1

[0186] Optimal determination of fetal chromosomal abnormalities using massively parallel DNA sequencing of cell-free fetal DNA from maternal blood: a test set 1 independent of the training set 1

[0187] This study was conducted by qualified site clinical investigators at 13 U.S. clinical sites between April 2009 and October 2010 as a scientific trial in human subjects approved by each institution's Institutional Review Board (IRB) planned. Written consent was obtained from each subject prior to participation in the study. The scientific trial program is designed to provide blood samples as well as clinical data to support the development of noninvasive prenatal genetic diagnostic methods. Pregnant women 18 years of age or older are eligible to participate. Blood was collected from patients undergoing clinically indicated chorionic villus sampling (CVS) or amniocentesis prior to the procedure, and results of fetal karyotype were also collected. Peripheral blood samples (two...

example 2

[0248] Validating aneuploidy determinations using multiple chromosome ratios: normalizing normalizing chromosomes

[0249] As described in previous examples, the method is based on the number of sequence tags mapped to the chromosome of interest for sequence tags mapped to samples exhibiting similar inter-sample and inter-run variability to the chromosome of interest The normalization of the number of . In order to validate the classification of aneuploidy and rule out that the normalizing chromosomes used in the analysis are themselves aneuploid chromosomes (i.e. present in abnormal copy numbers), the first normalizing chromosomes (i.e. used to determine chromosome dosage in Normalization for chromosomes) used to classify common aneuploidies involving chromosomes 21, 18, and X.

[0250] Using qualifying samples from training set 1 as described in Example 1, and qualifying samples from test set 1, the sequencing information was analyzed to identify at least one second normali...

example 3

[0279] Determine and verify chromosomal aneuploidy using at least two normalizing chromosomes for the chromosome of interest

[0280] To demonstrate that the determination of chromosomal aneuploidy can be validated by using the first and second normalizing chromosomes against the chromosome of interest, using chromosome 10 and chromosome 14 as the second and third normalizing against chromosome 21 of interest Normalizing Chromosome, Chromosome Dose for Chromosome 21 in Example 1A calculated using Chromosome 9 as the first Normalizing Chromosome.

[0281] FIG. 8A shows a plot of the NCVs for the 48 samples in test set 1 calculated using the mean and S.D. of the corresponding chromosome doses in the qualifying samples in training set 1 . The average CV % of chromosome dosage for chromosome 21 in training set 1 is provided in Table 7.

[0282] Table 7

[0283] Determination of the second normalizing chromosome for the chromosome of interest chromosome 21

[0284]

[0285] ...

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Abstract

The present invention provides a method capable of detecting single or multiple fetal chromosomal aneuploidies in a maternal sample comprising fetal and maternal nucleic acids, and verifying that the correct determination has been made. The method is applicable to determining copy number variations (CNV) of any sequence of interest in samples comprising mixtures of genomic nucleic acids derived from two different genomes, and which are known or are suspected to differ in the amount of one or more sequence of interest. The method is applicable at least to the practice of noninvasive prenatal diagnostics, and to the diagnosis and monitoring of conditions associated with a difference in sequence representation in healthy versus diseased individuals.

Description

field of invention [0001] The present invention provides a method capable of determining single or multiple fetal chromosomal aneuploidies in a maternal sample comprising fetal and maternal nucleic acid and verifying that the correct determination has been made. The method is suitable at least for the performance of non-invasive prenatal diagnosis, and for the diagnosis and monitoring of pathologies associated with differences in sequence expression in healthy versus diseased individuals. Background of the invention [0002] American College of Obstetrics and Gynecology (ACOG) Implementation Bulletin No. 77, published in 2007, supports the assessment of aneuploidy risk in all pregnant women in the first trimester based on cervical translucency measurements and Surrogate biochemical markers for screening for Down syndrome (ACOG Practice Bulletin No. 77, Obstet Gynecol 109:217-227 [2007]). These screening tests can only provide a risk determination which is inconclusive and h...

Claims

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Application Information

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IPC IPC(8): C12Q1/68G16B20/10G16B20/20
CPCC12Q1/6883G06F19/18C12Q1/6809G16B20/00G16B20/20G16B20/10C12Q2535/122C12Q2537/16C12Q2539/113
Inventor 里查德·P·拉瓦
Owner VERINATA HEALTH INC
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