# US 12,190,998 B2 · Combined size- and count-based analysis of maternal plasma for detection of fetal subchromosomal aberrations > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 12,190,998 B2 - Document ID: US12190998B2 - Status: Granted - Kind: B2 - Application number: 16/387,049 - Filed: 2019-04-17 - Published: 2019-08-08 - Granted: 2025-01-07 - Earliest claimed: 2015-01-23 - Assignees: The Chinese University of Hong Kong - Applicants: The Chinese University of Hong Kong - Inventors: Yuk-Ming Dennis Lo; Rossa Wai Kwun Chiu; Kwan Chee Chan; Peiyong Jiang; Cheuk Yin Jandy Yu - Web page: https://patentgrep.com/patent/US12190998B2 ## CPC - G16B 20/10: Ploidy or copy number detection - C12Q 1/6883: for diseases caused by alterations of genetic material - G16B 20/00: ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations - G16B 20/20: Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection - G16B 30/00: ICT specially adapted for sequence analysis involving nucleotides or amino acids - G16B 40/00: ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding - G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY - C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES ## Abstract An aberration in a fetal genome can be identified by analyzing a sample of fetal and maternal DNA. Classifications of whether an aberration (amplification or deletion) exists in a subchromosomal region are determined using count-based and size-based methods. The count classification and the size classification can be used in combination to determine whether only the fetus or only the mother, or both, have the aberration in the subchromosomal region, thereby avoiding false positives when the mother has the aberration and the fetus does not. ## Claims ### Claim 1 A method of identifying a subchromosomal copy number aberration in a fetal genome of a fetus by analyzing a biological sample from a female subject pregnant with the fetus, the biological sample including cell-free DNA molecules from the female subject and the fetus, the method comprising: for each of a plurality of DNA molecules in the biological sample: identifying a location of the DNA molecule in a reference genome, thereby obtaining locations of the plurality of DNA molecules; for each of a plurality of non-overlapping bins in the reference genome: measuring a respective amount of the plurality of DNA molecules located in a respective non-overlapping bin using the locations of the plurality of DNA molecules, computing a respective bin count parameter from the respective amount, and comparing the respective bin count parameter to one or more bin count thresholds to determine a bin count classification of the respective non-overlapping bin; performing, using a computer system, a segmentation process that merges consecutive non-overlapping bins into a merged segment based on the consecutive non-overlapping bins having a same bin count classification; comparing a length of the merged segment to a length threshold; computing a count parameter for the merged segment from bin count parameters of the non-overlapping bins of the merged segment or from amounts of the plurality of DNA molecules located in the non-overlapping bins of the merged segment; comparing the count parameter to one or more deviation thresholds to determine a count classification; classifying the fetus at risk of having the aberration in a subchromosomal region corresponding to the merged segment based on the comparison of the length of the merged segment to the length threshold and the count classification; and testing the fetus to confirm the subchromosomal copy number aberration. ### Claim 2 (depends on 1) The method of claim 1, wherein the segmentation process includes at least one of: a binary circular segmentation and a Hidden Markov model. ### Claim 3 (depends on 1) The method of claim 1, wherein the bin count classification is over-represented or under-represented. ### Claim 4 (depends on 1) The method of claim 1, wherein the aberration is a deletion or a duplication. ### Claim 5 (depends on 1) The method of claim 1, wherein the fetus is determined to have an amplification in the subchromosomal region when the count parameter is greater than a deviation threshold of the one or more deviation thresholds. ### Claim 6 (depends on 1) The method of claim 1, wherein the fetus is determined to have a deletion in the subchromosomal region when the count parameter is less than a deviation threshold of the one or more deviation thresholds. ### Claim 7 (depends on 1) The method of claim 1, wherein the non-overlapping bins are of an equal size. ### Claim 8 (depends on 1) The method of claim 1, wherein the non-overlapping bins exclude bins with a mappability less than a predetermined percentage. ### Claim 9 (depends on 1) The method of claim 1, wherein measuring the respective amount comprises using a GC correction. ### Claim 10 (depends on 1) The method of claim 1, wherein computing the respective bin count parameter comprises calculating a z-score, and wherein the z-score comprises using an amount determined from a group of healthy pregnancies carrying euploid fetuses. ### Claim 11 (depends on 1) The method of claim 1, wherein the one or more bin count thresholds are greater than a deviation threshold of the one or more deviation thresholds. ### Claim 12 (depends on 1) The method of claim 1, wherein the count parameter for the merged segment is from the amounts of the plurality of DNA molecules located in the non-overlapping bins of the merged segment. ### Claim 13 (depends on 12) The method of claim 12, further comprising: determining that the fetus and the female subject have the aberration when the count parameter is above a deviation threshold of the one or more deviation thresholds. ### Claim 14 (depends on 12) The method of claim 12, further comprising: determining a fetal DNA fraction in the biological sample, and determining the one or more deviation thresholds using the fetal DNA fraction. ### Claim 15 (depends on 14) The method of claim 14, further comprising: comparing the count parameter to a first deviation threshold and a second deviation threshold of the one or more deviation thresholds, and when the count parameter is greater than the first deviation threshold and less than the second deviation threshold: determining the fetus has the aberration, and determining the female subject does not have the aberration. ### Claim 16 (depends on 14) The method of claim 14, further comprising: comparing the count parameter to a first deviation threshold and a second deviation threshold of the one or more deviation thresholds, and when the count parameter is greater than the first deviation threshold and greater than the second deviation threshold: determining the female subject has the aberration. ### Claim 17 A computer product comprising a computer readable medium storing a plurality of instructions that when executed control a computer system to perform a method of identifying a subchromosomal copy number aberration in a fetal genome of a fetus, the method comprising: for each of a plurality of DNA molecules in a biological sample from a female subject pregnant with the fetus, the biological sample including cell-free DNA molecules from the female subject and the fetus: identifying a location of the DNA molecule in a reference genome, thereby obtaining locations of the plurality of DNA molecules; for each of a plurality of non-overlapping bins in the reference genome: measuring a respective amount of the plurality of DNA molecules located in a respective non-overlapping bin using the locations of the plurality of DNA molecules, computing a respective bin count parameter from the respective amount, and comparing the respective bin count parameter to one or more bin count thresholds to determine a bin count classification of the respective non-overlapping bin; performing a segmentation process that merges consecutive non-overlapping bins into a merged segment based on the consecutive non-overlapping bins having a same bin count classification; comparing a length of the merged segment to a length threshold; computing a count parameter for the merged segment from bin count parameters of the non-overlapping bins of the merged segment or from amounts of the plurality of DNA molecules located in the non-overlapping bins of the merged segment; comparing the count parameter to one or more deviation thresholds to determine a count classification; classifying the fetus at risk of having a copy number aberration in a subchromosomal region corresponding to the merged segment based on the comparison of the length of the merged segment to the length threshold and the count classification; and testing the fetus to confirm the subchromosomal copy number aberration. ### Claim 18 (depends on 1) The method of claim 1, wherein the plurality of DNA molecules comprises at least 20 million molecules. ### Claim 19 (depends on 1) The method of claim 1, wherein the reference genome is a human reference genome. ### Claim 20 (depends on 1) The method of claim 1, further comprising: determining, by the computer system, a size classification for the merged segment by: calculating a first statistical value of sizes of DNA molecules located in the merged segment; calculating a reference statistical value of sizes of DNA molecules located in a reference region; determining a separation value between the first statistical value and the reference statistical value; and comparing the separation value to one or more size thresholds to obtain the size classification; wherein determining whether the fetus has the aberration in the subchromosomal region corresponding to the merged segment is further based on the size classification. ### Claim 21 A method of identifying a subchromosomal copy number aberration in a fetal genome of a fetus by analyzing a biological sample from a female subject pregnant with the fetus, the biological sample including cell-free DNA molecules from the female subject and the fetus, the method comprising: for each of a plurality of DNA molecules in the biological sample: identifying a location of the DNA molecule in a reference genome by hybridizing the DNA molecule to a panel of probes with known chromosomal origin, thereby obtaining locations of the plurality of DNA molecules; for each of a plurality of non-overlapping bins in the reference genome: measuring a respective amount of the plurality of DNA molecules located in a respective non-overlapping bin using the locations of the plurality of DNA molecules, computing a respective bin count parameter from the respective amount, and comparing the respective bin count parameter to one or more bin count thresholds to determine a bin count classification of the respective non-overlapping bin; performing, using a computer system, a segmentation process that merges consecutive non-overlapping bins into a merged segment based on the consecutive non-overlapping bins having a same bin count classification; comparing a length of the merged segment to a length threshold; computing a count parameter for the merged segment from bin count parameters of the non-overlapping bins of the merged segment or from amounts of the plurality of DNA molecules located in the non-overlapping bins of the merged segment; comparing the count parameter to one or more deviation thresholds to determine a count classification; classifying the fetus at risk of having the aberration in a subchromosomal region corresponding to the merged segment based on the comparison of the length of the merged segment to the length threshold and the count classification; and testing the fetus to confirm the subchromosomal copy number aberration. ### Claim 22 (depends on 17) The computer product of claim 17, wherein each bin of the plurality of non-overlapping bins has a size from 500 kb to 2 Mb.