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`INFORMATION DISCLOSURE|[55 Named Inventor
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`Filing Date
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`INFORMATION DISCLOSURE First Named Inventor|AmirAli TALASAZ
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`STATEMENT BY APPLICANT
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`16/672,267 - GRU: 1637
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`Application Number
`16672267
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`2012) 5, 887-900
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`Examiner Name
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`PINKEL, et al. Comparative Genomic Hybridization. Annual Review of Genomics and Human Genetics, 6: 331-354
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`POLLACK,et al. Genome-wide analysis cof DNA copy-number changes using cDNA microarrays. Nat Genet. 1999
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`QIU, et al. DNA sequence-based "bar codes"for tracking the origins of expressed sequence tags from a maize cDNA
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`QUAIL, et al. A large genome center's improvementsto the Illumina sequencing system. Nat Methods. 2008 Dec;5
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`QUINLAN, A.R.et al., “Pyrobayes: an improved basecaller for SNP discovery in pyrosequences,” Nat. Methods 2008
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`RIZZO, J.M. et al. “Key Principles and Clinical Applications of ‘Next Generation’ DNA Sequencing,” Cancer Prev. Res.,
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`EFS Web 2.1.18
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`ALL REFERENCES CONSIDERED EXCEPT WHERE LINED THROUGH.
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`16/672,267 - GRU: 1637
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`Application Number
`16672267
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`Filing Date
`2019-11-01
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`INFORMATION DISCLOSURE First Named Inventor|AmirAli TALASAZ
`
`STATEMENT BY APPLICANT
`Art Unit
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`( Not for submission under 37 CFR 1.99)
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` Attorney Docket Number
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`SEBAT, et al. Large-Scale Copy Number Polymorphism in the Human Genome. Science, 305: 525-528 (2004).
`_—_=_=~oa
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`RYAN, et al. A prospective study of circulating mutant KRAS2 in the serum of patients with colorectal neoplasia: strong
`prognostic indicator in postoperative follow up. Gut. 2003 Jan:52(1}:101-8.
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`RYGAARD, et al. Abnormalities in structure and expression of the retinoblastoma gene in small cell lung cancercell
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`SAUSEN, M. et al. "Integrated genomic analyses identify ARID1A and ARID1B alterations in the childhood cancer
`euroblastoma", Nature Genetics 2013, 45(1), 12-17
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`SCHMITTet al. Supplemental Information http/Avww.pnas.org/content/suppl/20 12/08/01/1208715109.
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`SCHMITT,et al. Detection of ultra-rare mutations by next-generation sequencing. Proc Natl Acad Sci US A. 2012 Sep
`H-109(36):14508-13. doi: 10.1073/pnas.1208715109. Epub 2012 Aug 1.
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`SCHWARZENBACH, etal. A critical evaluation of loss of heterozygosity detected in tumortissues, blood serum and
`bone marrow plasma from patients with breast cancer. Breast Cancer Res. 2007;9(5)-R66.
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`5 CHWARZENBACH, etal. Cell-free tumor DNAin blocd plasma as a markerforcirculating tumorcells in prostate
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`SCHWARZENBACK,H. etal. "Cell-free nucleic acids as biomarkers in cancer patients" Nature Reviews Cancer
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`SCHWEIGER etal., “Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE}
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`EFS Web 2.1.18
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`16/672,267 - GAU: 1637
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`Application Number 16672267
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`
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`Filing Date 2019-11-01
`
`INFORMATION DISCLOSURE
`First Named Inventor|AmirAli TALASAZ
`STATEMENT BY APPLICANT
`( Not for submission under 37 CFR 1.99)
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`Art Unit |
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`Examiner Name
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` Attorney Docket Number
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`pbiochemotherapy. Clin Cancer Res. 2007 Apr 1:13(7):2068-74.
`pidemiol Biomarkers Prev. 1994 Jan-Feb;3(1):6/-71.
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`SEHNERT, A.J. et al. "Optimal Detection of Fetal Chromosomal Abnormalities by Massively Parallel DNA Sequencing
`bf Cell-Free Fetal DNA from Maternal Blood" Clin Chem (2011) 57(7):1042-1049
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`SHAW et al. Genomic analysis of circulating cell-free DNAinfers breast cancer dormancy. Genome Research 22
`2):220-231 (February 2012).
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`SHAW,et al. Microsatellite alterations plasma DNAof primary breast cancer patients. Clin Cancer Res. 2000 Mar;6
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`SHENDURE,J. et al. “Next-generation DNA sequencing,” Nat. Biotechnol. 2008 26(10), 1135-1145
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`BHINOZAKI, et al. Utility of circulating B-RAF DNA mutation in serum for monitoring melanoma patients receiving
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`SHIROGUCHI, et al. Digital RNA sequencing minimizes sequence-dependentbias and amplification noise with
`Dptimized single-molecule barcodes. Proc Natl Acad Sci US A. 2012 Jan 24;109(4):1347-52. doi: 10.1073/
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`SIMPSON, et al. Copy numbervariant detection in inbred strains from short read sequence data. Bioinformatics. 2010
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`SMITH, et al. Highly-multiplexed barcode sequencing: an efficient methodfor parallel analysis of pooled samples.
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`SMITH, T.F. et al. "Comparison of Biosequences" Adv App Math (1981) 2:482-489
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`ww
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`EFS Web 2.1.18
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`16/672,267 - GAU: 1637
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`Application Number 16672267
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`
`
`Filing Date 2019-11-01
`
`INFORMATION DISCLOSURE
`First Named Inventor|AmirAli TALASAZ
`STATEMENT BY APPLICANT
`( Not for submission under 37 CFR 1.99)
`
`
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`Art Unit |
`
` Attorney Docket Number
`
`
` | 42534-708.304
`Blage Il colon cancer,”Sci. Transl. Med. 2016, 8(346):346ra92
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`Examiner Name
`
`wwwa
`
`wao
`
`>awwwwoS©co~
`>>WwNo=
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`SPARKS, et al. Selective analysis of cell-free DNA in maternal blood for evaluation of fetal trisomy. Prenat Diagn. 2012
`an;32(1):3-9. doi: 10.1002/pd.2922. Epub 2012 Jan 6
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`STEINMAN. Free DNAin serum and plasma from normal adults. J Clin Invest. 1975 Aug;56(2):512-5.
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`STITZIEL, et al. Computational and statistical approaches to analyzing variants identified byexome sequencing.
`enomeBiol. 2011 Sep 14;12(9):227. doi: 10.1186/gb-2011-12-9-227.
`
`Stroun, M, et al, "About the possible orgin and mechanism ofcirculating DNA apoptosis and active DNA release", Clin
`him Acta, vol. 313, No. 1-2, pp. 139-142, (2001).
`
`STUMM, M. et al. "Noninvasive prenatal detection of chromosomal aneuploidies using different next generation
`Bequencing strategies and algorithms” Prenatal Diagnosis (2012) 32:569-577
`
`ABACK,et al. Detection of tumor-specific genetic alterations in bone marrow from early-stage breast cancerpatients.
`ancer Res. 2003 Apr 15:63(8): 1884-7
`
`AN, et al. Genome-wide comparison of DNA hydroxymethylation in mouse embryonic stem cells and neural
`progenitor cells by a new comparative hMeDIP-seq method. Nucleic Acids Res. 2013 Apr,41(7):e84. doi: 10.1093/nar/
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`Bp23 by 454 amplicon sequencing. BMC Genomics. 2010 Apr 19:11:252. doi: 10.1186/1471-2164-11-252.
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`
`EFS Web 2.1.18
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`16/672,267 ~ GAU: 1637
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`Application Number 16672267
`
`
`Filing Date 2019-11-01
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`INFORMATION DISCLOSURE First Named Inventor|AmirAli TALASAZ
`
`STATEMENT BY APPLICANT
`|...
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`( Not for submission under 37 CFR 1.99)
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`Examiner Name
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` Attorney Docket Number
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`| 42534-708.304
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`OMAZ,et al. Differential methylation as a cause of allele dropout at the imprinted GNASlocus. Genet Test Mol
`iomarkers. 2010 Aug; 14{4):455-60. doi: 10.1089/gtmb.2010.0029.
`
`OMLINSON, et al. A genome-wide association scan of tag SNPsidentifies a susceptibility variant for colorectal
`ancer at 8q?4 21. Nat Genet. 2007 Aug;39(8) 984-8. Epub 2007 Jul 8.
`
`SAI, et al. Discovery of rare mutations in populations: TILLING by sequencing. Plant Physiol. 2011 Jul;156
`3):1257-68. doi: 10.1104/pp.110.169748. Epub 2011 Apr 29.
`
`S. Appn. No. 14/102,285, filed 12/10/2013
`
`.9. Provisional Application 61/613,413 (Schmitt '413 provisional”) (2012-03-20)
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`9. Provisional Application 61/625,319 (Schmitt '319 provisional”) (2012-04-17)
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`16/672,267 ~ GAU: 1637
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`Application Number 16672267
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`Filing Date 2019-11-01
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`INFORMATION DISCLOSURE First Named Inventor|AmirAli TALASAZ
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