Rare cell analysis using sample splitting and DNA tags
IPC분류정보
국가/구분
United States(US) Patent
등록
국제특허분류(IPC7판)
C12Q-001/68
C12P-019/34
B01L-003/00
출원번호
US-0835926
(2013-03-15)
등록번호
US-9017942
(2015-04-28)
발명자
/ 주소
Shoemaker, Daniel
Kapur, Ravi
Toner, Mehmet
Stoughton, Roland
Davis, Ronald W.
출원인 / 주소
The General Hospital Corporation
대리인 / 주소
Fish & Richardson P.C.
인용정보
피인용 횟수 :
1인용 특허 :
202
초록▼
The present invention provides systems, apparatuses, and methods to detect the presence of fetal cells when mixed with a population of maternal cells in a sample and to test fetal abnormalities, e.g. aneuploidy. The present invention involves labeling regions of genomic DNA in each cell in said mixe
The present invention provides systems, apparatuses, and methods to detect the presence of fetal cells when mixed with a population of maternal cells in a sample and to test fetal abnormalities, e.g. aneuploidy. The present invention involves labeling regions of genomic DNA in each cell in said mixed sample with different labels wherein each label is specific to each cell and quantifying the labeled regions of genomic DNA from each cell in the mixed sample. More particularly the invention involves quantifying labeled DNA polymorphisms from each cell in the mixed sample.
대표청구항▼
1. A method for determining a presence or absence of a fetal aneuploidy of a fetus in a maternal blood sample from a woman who is pregnant or who is suspected of being pregnant, the method comprising: (a) obtaining a mixture of fetal and maternal genomic DNA from the maternal blood sample;(b) conduc
1. A method for determining a presence or absence of a fetal aneuploidy of a fetus in a maternal blood sample from a woman who is pregnant or who is suspected of being pregnant, the method comprising: (a) obtaining a mixture of fetal and maternal genomic DNA from the maternal blood sample;(b) conducting whole genome amplification of the mixture of fetal and maternal genomic DNA of (a) to obtain amplified nucleic acid molecules;(c) conducting ultra-deep sequencing of the amplified nucleic acid molecules obtained in step (b) to produce sequence data representing the complete genome for analysis, wherein ultra-deep sequencing comprises further amplification of the amplified nucleic acid molecules to produce at least one million copies of individual amplified nucleic acid molecules in parallel;(d) using the sequence data of (c) to quantify DNA regions of at least one chromosome being tested for aneuploidy and of at least one control chromosome that is presumed to be diploid, wherein the quantifying comprises analyzing the sequence data of (c) using computer executable logic recorded on a computer readable medium and executed by a processor; and(e) determining the presence or absence of a fetal aneuploidy for the at least one chromosome being tested for aneuploidy from quantification of the chromosomal DNA regions of (d). 2. The method of claim 1, wherein ultra-deep sequencing comprises sequencing-by-synthesis. 3. The method of claim 2, wherein sequencing-by-synthesis involves synthesizing nucleic acid strands complementary to the amplified nucleic acid molecules and inferring nucleic acid sequences of the amplified nucleic acid molecules from the complementary synthesized nucleic acid strands. 4. The method of claim 1, wherein the fetal aneuploidy comprises monosomy, trisomy, tetrasomy, or pentasomy of one or more chromosomes. 5. The method of claim 4, wherein the one or more chromosomes are sex chromosomes. 6. The method of claim 4, wherein the fetal aneuploidy comprises trisomy. 7. The method of claim 6, wherein trisomy comprises trisomy 13, trisomy 18, or trisomy 21. 8. The method of claim 4, wherein monosomy comprises monosomy X. 9. The method of claim 1, wherein the at least one chromosome being tested for aneuploidy is selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, chromosome X, and chromosome Y. 10. The method of claim 1, wherein each of the amplified nucleic acid molecules generated by whole genome amplification comprises a tag. 11. The method of claim 10, wherein the tag comprises a sequencing element. 12. The method of claim 11, wherein the sequencing element is about 4, 6, 8, 10, 18, 20, 28, 36, 46, or 50 nucleotide bases in length. 13. The method of claim 11, wherein the ultra-deep sequencing comprises sequencing-by-synthesis initiated using sequencing primers complementary to the sequencing element. 14. The method of claim 3, wherein sequencing-by-synthesis comprises detecting an identity of each nucleotide immediately after or upon incorporation of a labeled nucleotide or nucleotide analog into a growing nucleic acid strand complementary to the amplified nucleic acid molecules. 15. The method of claim 2, wherein sequencing-by-synthesis generates at least 1,000, at least 5,000, at least 10,000, at least 20,000, at least 30,000, at least 40,000, at least 50,000, at least 100,000, or at least 500,000 reads per hour. 16. The method of claim 15, wherein the reads have at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 120, or at least 150 bases per read. 17. The method of claim 1, wherein ultra-deep sequencing comprises sequencing by ligation. 18. The method of claim 17, wherein sequencing by ligation comprises a four-color sequencing by ligation. 19. The method of claim 18, wherein sequencing by ligation comprises hybridizing an anchor primer to one of four positions on the amplified nucleic acid molecules. 20. The method of claim 17, wherein sequencing by ligation comprises an enzymatic ligation reaction. 21. The method of claim 1, wherein the amplified nucleic acid molecules of (b) are mixed with beads such that a single amplified nucleic acid molecule attaches to a bead, and wherein ultra-deep sequencing of (c) comprises further amplification of the amplified nucleic acid molecule attached to a bead to produce the at least one million copies of the amplified nucleic acid molecule attached to each bead. 22. The method of claim 21, wherein the amplified nucleic acid molecule attached to each bead is amplified by polymerase chain reaction (PCR). 23. The method of claim 22, wherein the beads are placed into a highly parallel sequencing-by-synthesis machine that generates over 400,000 reads in a single 4 hour run. 24. The method of claim 23, wherein the at least one chromosome being tested for aneuploidy is selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, chromosome X, and chromosome Y.
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Hillman Robert S. (Cupertino CA) Cobb Michael E. (Sunnyvale CA) Allen Jimmy D. (Los Altos CA) Gibbons Ian (Menlo Park CA) Ostoich Vladimir E. (San Jose CA) Winfrey Laura J. (Belmont CA), Capillary flow device.
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Pourahmadi, Farzad; McMillan, William A.; Ching, Jesus; Chang, Ronald; Christel, Lee A.; Kovacs, Gregory T. A.; Northrup, M. Allen; Petersen, Kurt E., Device incorporating a microfluidic chip for separating analyte from a sample.
Hansmann Douglas D. ; Grace John P. ; Lowery Michael G. ; Oosta Gary M. ; Loomis Neil W. ; Shain Eric B. ; Schapira Thomas G., Devices and methods utilizing arrays of structures for analyte capture.
Hansmann Douglas D. ; Grace John P. ; Lowery Michael G. ; Oosta Gary M. ; Loomis Neil W. ; Shain Eric B. ; Schapira Thomas G., Devices and methods utilizing arrays of structures for analyte capture.
Asgari Morteza (Houston TX) Blick Mark (Houston TX) Bresser Joel (Bellaire TX) Cubbage Michael L. (Houston TX) Prashad Nagindra (Houston TX), Enriching and identifying fetal cells in maternal blood for in situ hybridization.
Asgari Morteza ; Blick Mark ; Bresser Joel ; Cubbage Michael Lee ; Prashad Nagindra, Enriching and identifying fetal cells in maternal blood for in situ hybridization on a solid surface.
Kbler Ulrich (Munich DEX) Hoffman Rainer (Frstenfeldbruck DEX), Extraction and cultivation of transformed cells and production of antibodies directed against them.
Asgari Morteza ; Blick Mark ; Bresser Joel ; Cubbage Michael Lee ; Prashad Nagindra, Intracellular antigens for identifying fetal cells in maternal blood.
Mehta, Tammy Burd; Kopf-Sill, Anne R.; Parce, J. Wallace; Chow, Andrea W.; Bousse, Luc J.; Knapp, Michael R.; Nikiforov, Theo T.; Gallagher, Steve, Manipulation of microparticles in microfluidic systems.
Douglass, James W.; Riding, Thomas J.; Ring, James E.; McLaren, Gina; Decker, William J.; Ellis, Robert T., Method and apparatus for automated image analysis of biological specimens.
Zld Tibor (Philippistrasse 13 4400 Mnster DEX), Method and apparatus for fast, reliable, and environmentally safe dispensing of fluids, gases and individual particles o.
Yourno Joseph (1662 New Scotland Rd. Slingerlands NY 12159), Method and apparatus for nested polymerase chain reaction (PCR) with single closed reaction tubes.
Fodstad .O slashed.ystein,NOX ; H.o slashed.if.o slashed.dt Hanne Kleppe,NOX ; Rye Philip,NOX, Method and device for detection of specific target cells in specialized or mixed cell populations and solutions containing mixed cell populations.
J. Michael Ramsey ; Robert S. Foote, Method for analyzing nucleic acids by means of a substrate having a microchannel structure containing immobilized nucleic acid probes.
Fodstad .O slashed.ystein,NOX ; Kvalheim Gunnar,NOX, Method for detection of specific target cells in specialized or mixed cell population and solutions containing mixed cell populations.
Fodstad, Øystein; Kvalheim, Gunnar, Method for detection of specific target cells in specialized or mixed cell population and solutions containing mixed cell populations.
Sammons David W. (Tucson AZ) Manley Michael (Tucson AZ) Utermohlen Joseph G. (Tucson AZ) Twitty Garland E. (Tucson AZ), Method for enrichment of fetal cell population from maternal whole blood samples.
Wang Yuzhou (Wayne PA) Tang Weixin (Landsdale PA) Cronin William J. (Matawan NJ) Liberti Paul A. (Huntingdon Valley PA), Method for magnetic separation featuring magnetic particles in a multi-phase system.
Saunders Alexander M. (San Carlos CA) Zarowitz Michael A. M. (San Carlos CA) Baldwin Patricia J. (Sunnyvale CA), Method for separating rare cells from a population of cells.
Lapidus Stanley N. (Bedford NH) Shuber Anthony P. (Milford MA) Ulmer Kevin M. (Cohasset MA), Method for the detection of clonal populations of transformed cells in a genomically heterogeneous cellular sample.
Rimm David L. ; Levine Robert A. ; Wardlaw Stephen C. ; Fiedler Paul, Method for the detection, identification, enumeration and confirmation of circulating cancer and/or hematologic progenitor cells in whole blood.
Fodstad,Oystein; Kvalbeim,Gunnar; Wang,Meng yu; Engebraten,Olav; Juell,Siri, Method of killing target cells in harvested cell populations with one or more immuno-toxins.
Brown James F. ; Silver Jonathan E. ; Kalinina Olga V.,CAX, Method of sampling, amplifying and quantifying segment of nucleic acid, polymerase chain reaction assembly having nanoliter-sized sample chambers, and method of filling assembly.
James F. Brown ; Jonathan E. Silver ; Olga V. Kalinina CA, Method of sampling, amplifying and quantifying segment of nucleic acid, polymerase chain reaction assembly having nanoliter-sized sample chambers, and method of filling assembly.
Wilding Peter (Paoli PA) Kricka Larry J. (Berwyn PA) Zemel Jay N. (Jenkintown PA), Methods and apparatus for the detection of an analyte utilizing mesoscale flow systems.
Leon W. M. M. Terstappen ; Galla Chandra Rao ; Jonathan W. Uhr ; Emilian V. Racila ; Paul A. Liberti, Methods and reagents for the rapid and efficient isolation of circulating cancer cells.
Terstappen, Leon W. M. M.; Rao, Galla Chandra; Uhr, Jonathan W.; Racila, Emilian V.; Liberti, Paul A., Methods and reagents for the rapid and efficient isolation of circulating cancer cells.
Terstappen Leon W. M. M. ; Liberti Paul A., Methods for biological substance analysis employing internal magnetic gradients separation and an externally-applied transport force.
Roche Patrick C. ; Klee George G. ; Limburg Paul J. ; Ahlquist David A., Methods of recovering colorectal epithelial cells or fragments thereof from stool.
Nelson, Robert J.; Hooper, Herbert H.; Hauser, Alan K.; Singh, Sharat; Williams, Stephen J.; Sassi, Alexander P., Microfluidic apparatus and method for purification and processing.
Nelson Robert J. ; Hooper Herbert H. ; Hauser Alan K. ; Singh Sharat ; Williams Stephen J. ; Sassi Alexander P., Microfluidic method for nucleic acid purification and processing.
Robert J. Nelson ; Herbert H. Hooper ; Alan K. Hauser ; Sharat Singh ; Stephen J. Williams ; Alexander P. Sassi, Microfluidic method for nucleic acid purification and processing.
Culbertson, Christopher T.; Jacobson, Stephen C.; McClain, Maxine A.; Ramsey, J. Michael, Microfluidic systems and methods of transport and lysis of cells and analysis of cell lysate.
Austin Robert H. (Princeton NJ) Volkmuth Wayne D. (Menlo Park MN) Rathburn Lynn C. (Ithaca NY), Microlithographic array for macromolecule and cell fractionation.
Dennis, Lo Yuk Ming; Man, Poon Lit, Non-invasive methods for detecting non-host DNA in a host using epigenetic differences between the host and non-host DNA.
Lee Allan Christel ; Gregory T. A. Kovacs ; William A. McMillan ; M. Allen Northrup ; Kurt E. Petersen ; Farzad Pourahmadi, Non-planar microstructures for manipulation of fluid samples.
Hollis Mark A. ; Ehrlich Daniel J. ; Murphy R. Allen ; Kosicki Bernard B. ; Rathman Dennis D. ; Mathews Richard H. ; Burke Barry E. ; Eggers Mitch D. ; Hogan Michael E. ; Varma Rajender Singh, Optical and electrical methods and apparatus for molecule detection.
Niimura Toshinobu (Mineola NY) Takahashi Tadashi (Port Washington NY) Kashiba Mutsuro (Williston Park NY) Sakai Ko (Hew Hyde Park NY) Kano Tokio (Bellerose NY), Plate substrate immunoassay device and method for performing a multi-test immunoassay on a specimen.
Mullis Kary B. (La Jolla CA) Erlich Henry A. (Oakland CA) Arnheim Norman (Woodland Hills CA) Horn Glenn T. (Emeryville CA) Saiki Randall K. (Richmond CA) Scharf Stephen J. (Berkeley CA), Process for amplifying, detecting, and/or cloning nucleic acid sequences.
Choi, Gil H.; Kunsch, Charles A.; Barash, Steven C.; Dillon, Patrick J.; Dougherty, Brian; Fannon, Michael R.; Rosen, Craig A., Streptococcus pneumoniae antigens and vaccines.
Wetzel,Arthur W.; Gilbertson, II,John R.; Beckstead,Jeffrey A.; Feineigle,Patricia A.; Hauser,Christopher R.; Palmieri, Jr.,Frank A., System and method for finding regions of interest for microscopic digital montage imaging.
Pall David B. (Roslyn Estates NY) Gsell Thomas C. (Glen Cove NY) Matkovich Vlado I. (Glen Cove NY) Bormann Thomas (Seaford NY), System for processing biological fluid.
Sammons David W. ; Twitty Garland E. ; Utermohlen Joseph G. ; Sharnez Rizwan, System for separation of nucleated fetal erythrocytes from maternal blood samples.
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