Non-invasive prenatal diagnosis of fetal genetic condition using cellular dna and cell free dna

Abstract

Disclosed are methods for determining at least one sequence of interest of a fetus of a pregnant mother. In various embodiments, the method can determine one or more sequences of interest in a test sample that comprises a mixture of maternal cellular DNA and mother-and-fetus cfDNA. In some embodiments, methods are provided for determining whether the fetus has a genetic disease. In some embodiments, methods are provided for determining whether the fetus is homozygous in a disease causing allele when the mother is heterozygous of the same allele. In some embodiments, methods are provided for determining whether the fetus has a copy number variation (CNV) or a non-CNV genetic sequence anomaly.

1 - 60 . (canceled) 
     
     
         61 . A system for use in determining a condition of a fetus related to a sequence of interest using maternal cellular DNA and mixed cfDNA from a maternal sample, the system including a sequencer for receiving a nucleic acid sample and providing fetal and maternal nucleic acid sequence information from the sample; a processor; and a machine readable storage medium comprising instructions for execution on said processor, the instructions comprising:
 code for obtaining sequence reads of mother-only cellular DNA obtained from the mother carrying the fetus, the cellular DNA having been specifically enriched for a sequence of interest;   code for computing a count of sequence tags mapping to the sequence of interest for the cellular DNA;   code for obtaining sequence reads of mother-and-fetus mixed cfDNA obtained from the mother, the cfDNA having been specifically enriched for the sequence of interest;   code for computing a count of sequence tags mapping to the sequence of interest for the cfDNA;   code for comparing the sequence tag counts mapping to the sequence of interest between the cellular DNA and the cfDNA; and   code for determining the condition of the fetus related to the sequence of interest.   
     
     
         62 . A computer system, comprising:
 one or more processors;   system memory; and   one or more computer-readable storage media having stored thereon computer-executable instructions that, when executed by the one or more processors, cause the computer system to implement a method for determining a condition of a fetus related to a sequence of interest, the method comprising:
 obtaining sequence reads of mother-only cellular DNA obtained from the mother carrying the fetus, the cellular DNA having been specifically enriched for a sequence of interest; 
 computing a count of sequence tags mapping to the sequence of interest for the cellular DNA; 
 obtaining sequence reads of mother-and-fetus mixed cfDNA obtained from the mother, the cfDNA having been specifically enriched for the sequence of interest; 
 computing a count of sequence tags mapping to the sequence of interest for the cfDNA; 
 comparing the sequence tag counts mapping to the sequence of interest between the cellular DNA and the cfDNA; and 
 determining the condition of the fetus related to the sequence of interest. 
   
     
     
         63 . The system of 61, wherein the specifically enriched cellular DNA and the specifically enriched cfDNA were combined for amplification and/or sequencing. 
     
     
         64 . The system of 63, wherein the specifically enriched cellular DNA and the specifically enriched cfDNA were combined in similar quantity. 
     
     
         65 . The system of 61, wherein code for determining the condition of the fetus related to the sequence of interest comprises code for determining a fetal zygosity of the sequence of interest. 
     
     
         66 . The system of 65, wherein the code for determining the fetal zygosity comprises code for determining that the mother is heterozygous and the fetus is homozygous. 
     
     
         67 . The system of 65, wherein the code for determining the fetal zygosity comprises code for determining a fetal fraction assuming the fetal zygosity. 
     
     
         68 . The system of  claim 61 , wherein code for determining the condition of the fetus related to the sequence of interest comprises code for determining whether the fetus has a genetic disease from the at least one sequence of interest of the fetus. 
     
     
         69 . The system of  claim 61 , wherein code for determining the condition of the fetus related to the sequence of interest comprises code for using a coverage quantity of sequence tags mapping to the sequence of interest derived from the mother-only cellular DNA to determine a zygosity of the sequence of interest for the fetus. 
     
     
         70 . The system of  claim 61 , wherein the at least one sequence of interest comprises a chromosome or a chromosome segment. 
     
     
         71 . The system of  claim 61 , wherein code for determining the condition of the fetus related to the sequence of interest comprises code for determining a complete or partial aneuploidy. 
     
     
         72 . The computer system of 62, wherein the specifically enriched cellular DNA and the specifically enriched cfDNA were combined for amplification and/or sequencing. 
     
     
         73 . The computer system of 72, wherein the specifically enriched cellular DNA and the specifically enriched cfDNA were combined in similar quantity. 
     
     
         74 . The computer system of 62, wherein determining the condition of the fetus related to the sequence of interest comprises determining a fetal zygosity of the sequence of interest. 
     
     
         75 . The computer system of 74, wherein determining the fetal zygosity comprises determining that the mother is heterozygous and the fetus is homozygous. 
     
     
         76 . The computer system of 74, wherein determining the fetal zygosity comprises determining a fetal fraction assuming the fetal zygosity. 
     
     
         77 . The computer system of  claim 62 , wherein determining the condition of the fetus related to the sequence of interest comprises determining whether the fetus has a genetic disease from the at least one sequence of interest of the fetus. 
     
     
         78 . The computer system of  claim 62 , wherein determining the condition of the fetus related to the sequence of interest comprises using a coverage quantity of sequence tags mapping to the sequence of interest derived from the mother-only cellular DNA to determine a zygosity of the sequence of interest for the fetus. 
     
     
         79 . The computer system of  claim 62 , wherein the at least one sequence of interest comprises a chromosome or a chromosome segment. 
     
     
         80 . The computer system of  claim 62 , wherein determining the condition of the fetus related to the sequence of interest comprises determining a complete or partial aneuploidy.