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Findings regarding the association between mitochondrial DNA (mtDNA) variants and Alzheimer's disease (AD) are inconsistent.    Methods  We developed a pipeline for accurate assembly and variant calling in mitochondrial genomes embedded within whole exome sequences (WES) from 10,831 participants from the Alzheimer's Disease Sequencing Project (ADSP). Association of AD risk was evaluated with each mtDNA variant and variants located in 1158 nuclear genes related to mitochondrial function using the SCORE test. Gene‐based tests were performed using SKAT‐O.    Results  Analysis of 4220 mtDNA variants revealed study‐wide significant association of AD with a rare  MT‐ND4L  variant (rs28709356 C>T; minor allele frequency = 0.002;  P  = 7.3 × 10 −5 ) as well as with  MT‐ND4L  in a gene‐based test ( P  = 6.71 × 10 −5 ). Significant association was also observed with a MT‐related nuclear gene,  TAMM41 , in a gene‐based test ( P  = 2.7 × 10 −5 ). The expression of  TAMM41  was lower in AD cases than controls ( P  = .00046) or mild cognitive impairment cases ( P  = .03).    Discussion  Significant findings in  MT‐ND4L  and  TAMM41  provide evidence for a role of mitochondria in AD.

Association of mitochondrial variants and haplogroups identified by whole exome sequencing with Alzheimer's disease