Table 1.

A summary of NGS short read sequencing studies in AD. Association statistically significant at p < 10⁻⁶ exome wide for WES and p < 10⁻⁸ genome-wide for Whole Genome Sequencing (WGS).

Author	Method	Cohort	Cohort Size (n)	Outcome
[21]	Agilent SureSelect Human & Illumina sequencing	Autosomal dominant EOAD without known mutations	14	7 unknown mutations detected in SORL1 gene.
[20]	WGS, Illumina bead chip, and imputation	Icelandic	1795 WGS 71743 chip	Coding mutation A673T in APP protects against AD.
[16]	WGS, Illumina bead chip, and imputation	Icelandic	1795 WGS	rs75932628-T (R47H) of TREM2 increases risk of LOAD.
[17]	Illumina WES TruSeq, Illumina Sequenced	Caucasian from UK, US and Canada	1092 AD cases 1107 Controls	rs75932628-T (R47H) of TREM2 increases risk of LOAD.
[14]	Roche NimbleGen v2 and v3, SeqCap® EZ Exome, Illumina TruSeq	1908 Dutch AD cases and Controls	640 cases 1268 Controls	181 unique SORL1 variants detected. Developed a strategy to classify SORL1 variants into five subtypes ranging from pathogenic to benign.
[22]	Targeted sequencing using Agilent HaloPLex™ and Illumina sequencing	Unrelated LOAD and matched controls	772 LOAD 757 Controls	Intronic variant rs78117248 in ABCA7 showed strongest association with AD. Loss of function mutations may be a potential pathogenic mechanism.
[18]	WGS and WES data generated by ADSP using Roche NimbleGen and Illumina Rapid Capture Exome	European-American and Hispanic	172 AD 171 Controls	Novel variants in previously reported AD risk genes and variants in novel genes IGHG3 and ZNF655 were detected.
[19]	Agilent SureSelect and ADSP using Roche NimbleGen and Illumina Rapid Capture Exome	Caucasian non APOE*4 carriers from PITT-ADRC 1 ADSP 2	PITT-ADRC1372 AD 348 Controls ADSP2 2113 AD 5139 Controls	Association at novel variant in NSF gene and known loci in TREM2, TOMM40 and APOE was detected.
[15]	Roche NimbleGen, Agilent NextEra, Truseq, HaloPlex, SureSelect, Illumina Nextera® Rapid Capture Exome	25982 Caucasian	12652 AD 8693 controls	Detected protein damaging variants in TREM2, SORL1 and ABCA7 and protective variants in CBX3 and PRSS3.
[23]	ADSP using Nimblegen NimbleGen v2 and v3 and Illumina Nextera® Rapid Capture Exome	5142	4889	Identified a VNTR within MUC6 associated with pTau burden.

¹: University of Pittsburgh Alzheimer’s Disease Research Center (ADRC). ²: Alzheimer’s Disease Sequencing Project (ADSP).