Use of off-target sequences for dna analysis
AssigneeAgilent Technologies Belgium S.A./N.V
InventorBenoit DEVOGELAERE
Life of this patent
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Abstract
The present teachings concern a method for determining the presence or absence of a fetal chromosomal aneuploidy and/or loss of heterozygosity (LOH) in a biological sample obtained from a pregnant female, the method comprising: obtaining sequence information indicative of targeted-capture massively parallel sequencing of the biological sample comprising both maternal and fetal nucleic acids; determining the amount of off-target reads obtained from said targeted capture massively parallel sequencing; and deriving from said off-target read counts information for determining the absence or presence of said aneuploidy or LOH.
Claims13
A method for determining the presence or absence of a fetal chromosomal aneuploidy and/or loss of heterozygosity (LOH) in a biological sample obtained from a pregnant female, the method comprising:
- obtaining sequence information indicative of targeted-capture massively parallel sequencing of the biological sample comprising both maternal and fetal nucleic acids;
- determining the amount of off-target reads obtained from said targeted capture massively parallel sequencing;
- and
- deriving from said off-target read counts information for determining the absence or presence of said aneuploidy or LOH.
A method for determining the presence or absence of a fetal aneuploidy and/or loss of heterozygosity (LOH) in biological sample of a pregnant female, said sample comprises both maternal and fetal cell-free DNA, the method comprising:
- a) obtaining maternal and fetal DNA from said biological sample;
- b) contacting said DNA with one or more labeled RNA or DNA probes, thereby allowing hybridization of said probes to said maternal or fetal DNA;
- c) capturing said hybridized DNA:probes;
- d) performing sequencing of said captured DNA, thereby obtaining reads;
- e) mapping said reads to a reference genome;
- f) separating the on- and off-target reads;
- g) obtaining off-targets read counts;
- and using said off-target read counts for determining the presence or absence of a fetal aneuploidy or LOH.
A method for detecting the presence of a loss-of-heterozygosity event in a biological sample obtained from a subject, said sample comprises nucleic acids, said method comprises the steps of:
- obtaining sequence information from a targeted-capture massively parallel sequencing of DNA obtained from said sample;
- determining the amount of off-target reads obtained from said targeted capture massively parallel sequencing;
- and
- deriving from said off-target read counts information for determining the absence or presence of said LOH.
Dependencies are inferred from the claim text.