US 11,781,187 B2
Rare cell analysis using sample splitting and DNA tags
Daniel Shoemaker, San Diego, CA (US); Mehmet Toner, Charlestown, MA (US); Ravi Kapur, Sharon, MA (US); Roland B. Stoughton, The Sea Ranch, CA (US); and Ronald W. Davis, Palo Alto, CA (US)
Assigned to The General Hospital Corporation, Boston, MA (US); GPB Scientific, LLC, Richmond, VA (US); and Verinata Health, Inc., Redwood City, CA (US)
Filed by The General Hospital Corporation, Boston, MA (US); GPB Scientific, LLC, Richmond, CA (US); and Verinata Health, Inc., Redwood City, CA (US)
Filed on Nov. 16, 2018, as Appl. No. 16/193,916.
Application 16/193,916 is a continuation of application No. 14/697,372, filed on Apr. 27, 2015, granted, now 10,155,984.
Application 14/697,372 is a continuation of application No. 13/835,926, filed on Mar. 15, 2013, granted, now 9,017,942.
Application 13/835,926 is a continuation of application No. 13/306,640, filed on Nov. 29, 2011, abandoned.
Application 13/306,640 is a continuation of application No. 12/230,628, filed on Sep. 2, 2008, granted, now 8,168,389, issued on May 1, 2012.
Application 12/230,628 is a continuation of application No. 11/763,421, filed on Jun. 14, 2007, granted, now 8,372,584, issued on Feb. 12, 2013.
Claims priority of provisional application 60/820,778, filed on Jul. 28, 2006.
Claims priority of provisional application 60/804,819, filed on Jun. 14, 2006.
Prior Publication US 2021/0062261 A1, Mar. 4, 2021
This patent is subject to a terminal disclaimer.
Int. Cl. C12Q 1/6869 (2018.01); C12Q 1/6883 (2018.01); C12Q 1/6809 (2018.01); C12Q 1/6881 (2018.01); G01N 15/10 (2006.01); B01L 3/00 (2006.01)
CPC C12Q 1/6883 (2013.01) [C12Q 1/6809 (2013.01); C12Q 1/6869 (2013.01); C12Q 1/6881 (2013.01); B01L 3/502761 (2013.01); C12Q 2600/156 (2013.01); C12Q 2600/158 (2013.01); C12Q 2600/16 (2013.01); G01N 2015/1006 (2013.01); G01N 2015/1087 (2013.01); Y10T 436/143333 (2015.01)] 33 Claims
 
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 cells from the maternal blood sample and dividing the mixture into discrete locations such that no more than one cell is located per discrete location;
(b) obtaining genomic DNA from fetal cells or maternal cells located within the discrete locations;
(c) conducting multiplex polymerase chain reaction (PCR) to amplify target regions in the genomic DNA to obtain amplified nucleic acid molecules, wherein each amplified nucleic acid molecule comprises a tag that identifies the nucleic acid molecule as coming from a specific discrete location;
(d) pooling the amplified nucleic acid molecules with tagged amplicons from at least one other multiplex PCR;
(e) conducting ultra-deep sequencing of the pooled amplified nucleic acid molecules obtained in step (d) to produce sequence data representing a partial genome for analysis of allele abundance, wherein the 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;
(f) using the sequence data of step (e) 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 step (e) using computer executable logic recorded on a computer readable medium and executed by a processor; and
(g) 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 step (f).