(12) Patent Application Publication (10) Pub. No.: US 2005/0123913 A1 Wallace Et Al
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US 2005O123913A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2005/0123913 A1 Wallace et al. (43) Pub. Date: Jun. 9, 2005 (54) HUMAN MITOCHONDRIAL DNA (57) ABSTRACT POLYMORPHISMS, HAPLOGROUPS, This invention provides human mtDNA polymorphisms that ASSOCATIONS WITH PHYSIOLOGICAL are diagnostic of all the major human haplogroups and CONDITIONS, AND GENOTYPING ARRAYS methods of diagnosing those haplogroupS and Selected Sub haplogroups. This invention also provides methods for iden tifying evolutionarily Significant mitochondrial DNA genes, (75) Inventors: Douglas C. Wallace, Irvine, CA (US); nucleotide alleles, and amino acid alleles. Evolutionarily Seyed Hosseini, Duluth, GA (US); Dan Significant genes and alleles are identified using one or two Mishmar, Irvine, CA (US); Eduardo populations of a Single species. The process of identifying Ruiz-Pesini, Irvine, CA (US); Marie evolutionarily Significant nucleotide alleles involves identi Lott, Atlanta, GA (US) fying evolutionarily significant genes and then evolution arily significant nucleotide alleles in those genes, and iden Correspondence Address: tifying evolutionarily Significant amino acid alleles involves Greenlee Winner & Sullivan identifying amino acids encoded by all nonsynonymous Suite 200 alleles. Synonymous codings of the nucleotide alleles 4875 Pearl East Circle encoding evolutionarily significant amino acid alleles of this Boulder, CO 80301 (US) invention are equivalent to the evolutionarily significant amino acid alleles disclosed herein and are included within (73) Assignee: Emory University, Atlanta, GA (US) the Scope of this invention. Synonymous codings include alleles at neighboring nucleotide loci that are within the (21) Appl. No.: 10/488,618 Same codon. This invention also provides methods for asSociating haplogroupS and evolutionarily significant (22) PCT Filed: Aug. 30, 2002 nucleotide and amino acid alleles with predispositions to physiological conditions. Methods for diagnosing predispo (86) PCT No.: PCT/US02/28471 Sition to LHON, and methods for diagnosing increased likelihood of developing blindness, centenaria, and Related U.S. Application Data increased longevity that are not dependent on the geographi cal location of the individual being diagnosed are provided (60) Provisional application No. 60/316,333, filed on Aug. herein. Diagnosis of an individual with a predisposition to an 30, 2001. Provisional application No. 60/380,546, energy metabolism-related physiological condition is depen filed on May 13, 2002. dent on the geographic region of the individual. Physiologi (30) Foreign Application Priority Data cal conditions diagnosable by the methods of this invention include healthy conditions and pathological conditions. Aug. 31, 2001 (CA)............................................. 2356536 Physiological conditions that are associated with haplo groupS and with alleles provided by this invention include Publication Classification energetic imbalance, metabolic disease, abnormal energy metabolism, abnormal temperature regulation, abnormal (51) Int. Cl." ............................ C12O 1/68; G06F 19/00; oxidative phosphorylation, abnormal electron transport, G01N 33/48; G01N 33/50 obesity, amount of body fat, diabetes, hypertension, and (52) U.S. Cl. ................................................... 435/6; 702/20 cardiovascular disease. Patent Application Publication Jun. 9, 2005 Sheet 1 of 5 US 2005/0123913 A1 -000'09'], 000'01), Patent Application Publication Jun. 9, 2005 Sheet 2 of 5 US 2005/0123913 A1 VZ(OIH Patent Application Publication Jun. 9, 2005 Sheet 3 of 5 US 2005/0123913 A1 004 Z? 004 004 Patent Application Publication Jun. 9, 2005 Sheet 4 of 5 US 2005/0123913 A1 iššião an on -> x a .55 ]ÕI ]ITI |ZT Patent Application Publication Jun. 9, 2005 Sheet 5 of 5 US 2005/0123.913 A1 aretatasaresearray Rese seases cease ersceases- Grossaea ease eye. Secessessesses ------- 5 - s 2. 83 2. S asses See assassissances aessels seasesses reassists Revastates LO v (Sy/ey)u=OX US 2005/O123913 A1 Jun. 9, 2005 HUMAN MITOCHONDRIAL DNA 22976; Wallace, D. C. (1999) “Mitochondrial Diseases in POLYMORPHISMS, HAPLOGROUPS, Man and Mouse'Science 283:1482–1488; Saraste, M. ASSOCATIONS WITH PHYSIOLOGICAL (1999) “Oxidative Phosphorylation at the fin de siecle CONDITIONS, AND GENOTYPING ARRAYS 'Science 283:1488-1493; Kokoszka et. al. (2001) “Increased mitochondrial oxidative stress in the Sod2 (+/-) mouse CROSS-REFERENCE TO RELATED results in the age-related decline of mitochondrial function APPLICATIONS culminating in increased apoptosis'PNAS 98:2278-2283; Wallace, D.C. (2001) Mental Retardation and Developmen 0001. This application claims priority to U.S. Patent tal Disabilities 7:158-166; Wallace, D. C. (2001) Am. J. Application Ser. No. 60/316,333 filed Aug. 30, 2001 and Ser. Med. Gen. 106:71-93; Wei, Y-H et al. (2001) Chinese No. 60/380,546 filed May 13, 2002, and to Canadian Patent Medical Journal (Taipei) 64:259-270; and Wallace, D. C. Application No. 2,356,536 filed on Aug. 31, 2001, which are hereby incorporated in their entirety by reference to the (2001) EuroMit 5 Abstract. extent not inconsistent with the disclosure herein. 0005 Certain mitochondrial mutations have been asso ciated with physiological conditions (U.S. Pat. No. 6,280, STATEMENT REGARDING FEDERALLY 966 issued on Aug. 28, 2001; U.S. Pat. No. 6,140,067 issued SPONSORED RESEARCH on Oct. 31, 2000; U.S. Pat. No. 5,670,320; U.S. Pat. No. 5,296,349; U.S. Pat. No. 5,185,244; U.S. Pat. No. 5,494,794; 0002 This invention was made in part with funding from Wallace, D. C. (1999) Science 283: 1482–1488; Brown, M. the United States Government (NIH grants AG 13154, D. et al. (2001) American Society for Human Genetics HL4017, NS21328, and NS37167). The United States Gov Poster #2332; Brown, M. D. et al., (2001) Human Genet. ernment may have certain rights therein. 109:33-39; and Brown, M. D. et al. (January 2002) Human Genet. 110:130-138), Wallace, D. C. et al. (1999) Gene BACKGROUND OF THE INVENTION 238:211-230 describes analysis of LHON mutants. Gross man, L. I. et al. (2001) Molecular Phylogenetics and Evo 0003) Human mitochondrial DNA (mtDNA) is mater lution 18(1):26-36, describes changes in the biochemical nally inherited. Mutations accumulate Sequentially in radi machinery for aerobic energy metabolism. Kalman, B. et al. ating lineages creating branches on the human evolutionary (1999) Acta Neurol. Scand. 99(1): 16-25 describes mito tree. Using Sequences of mtDNA, human populations are chondrial mutations and multiple sclerosis (MS). Wei, Y. H. divisible evolutionarily into haplogroups (Wallace, D. C. et et al. (2001) Chinese Medical Journal 64:259-270 describes al. (1999) Gene 238:211-230; Ingman M. et al., (2000) recent results in Support of the mitochondrial theory of Nature 408:708–713; Maca-Meyer, N. (August 2001) aging. BioMed Central 2:13; T. G. Schurr et al., (1999) American Journal of Physical Anthropology 108:1-39; and V. 0006 Ivanova, R. et al. (1998) Geronotology 44:349 Macaulay et al., (1999) American Journal of Human Genet describes mitochondrial haplotypes and longevity in a ics 64:232-249). Related haplogroups can be combined into French population. Tanaka, M. et al. (1998) Lancet 351:185 macro-haplogroups. Haplogroups can be Subdivided into 186 describes longevity and haplogroups in a Japanese Subhaplogroups. The complete Cambridge mitochondrial population. De Benedictis, G. et al. (1999) FASEB 13:1532 DNA sequence may be found at MITOMAP, http://www 1536 describes haplogroups and longevity in an Italian gen.emory.edu/cgi-gin/MITOMAP, Genbank accession no. population. Rose, G. et al. (2001) European Journal of J01415, and is provided in SEQ ID NO:2. Also see Andrews Human Genetics 9:701-707 describes haplogroup J in cen et al. (1999), “Reanalysis and Revision of the Cambridge tenarians. Ross, O. A. et al. (2001) Experimental Gerontol Reference Sequence for Human Mitochondrial DNA, Na ogy 36(7): 1161-1178 describes haplotypes and longevity in ture Genetics 23:147. an Irish population. 0004 Publications on the subject of mitochondrial biol 0007 Haplogroup T has been associated with reduced ogy include: Scheffler, I. E. (1999) Mitochondria, Wiley Sperm motility in European males (E. Ruiz-Pesini et al., Liss, NY; Lestienne P Ed., Mitochondrial Diseases. Models 2000 American Journal of Human Genetics 67:682-696), and Methods, Springer-Verlag, Berlin; Methods in Enzymol the tRNA"np 4336 variant in haplogroup H is associated ogy (2000) 322: Section V Mitochondria and Apoptosis, with late-onset Alzheimer Disease (J. M. Shoffner et al., Academic Press, CA; Mitochondria and Cell Death (1999) 1993 Genomics 17:171-184). Princeton University Press, NJ; Papa S, Ferrucio G, and Tager J Eds.; Frontiers of Cellular Bioenergetics. Molecular 0008 Taylor, R. W. (1997) J. of Bioenergetics and Biology, Biochemistry, and Physiopathology, Kluwer Aca Biomembranes 29(2):195-205 describes methods for treat demic/Plenum Publishers, NY; Lemasters, J. and Nieminen, ing mitochondrial disease. Colombet, J. and Coutelle, C. A. (2001) Mitochondria in Pathogenesis, Kluwer Academic/ (1998) Molecular Medicine Today 4(1):1-8 describes gene Plenum Publishers, NY; MITOMAP http://www.gen.emo therapy for mitochondrial disorders, including using cell ry.edu/cgi-gin/MITOMAP; Wallace, D.C. (2001) “A mito fusion to introduce healthy mitochondria. Owen, R. and chondrial paradigm for degenerative diseases and ageing Flotte, T. R. (2001) Antioxidants and Redox Signaling Novartis Foundation Symposium