Table 3: Quality assessment scores for each study.

Each study was scored across 10 quality assessment categories, with one (1) being the lowest (worst) score and three (3) being the highest (best) score. Definition of objective criteria for scoring each study can be found in Table 2.

Study	Sample size	Sex and ethnicity	AD diagnose criteria	Control matching	Transcript level analysis	Results validation	Sequencing depth	Statistical rigor	Data availability	Reproducibility	Average score per study (standard deviation)
Shmookler Reis et al.	1	1	1	1	1	3	1	1	1	1	1.2 (0.63)
Twine et al.	1	1	1	1	2	1	1	2	2	1	1.3 (0.48)
Mills et al.	1	1	1	2	2	2	1	2	2	1	1.5 (0.53)
Cho et al.	1	2	1	2	1	2	2	2	2	1	1.6 (0.52)
Jia et al.	1	2	2	1	1	2	3	2	1	1	1.6 (0.7)
Barbash et al.	1	1	2	2	1	2	3	1	2	1	1.6 (0.7)
Lee et al.	1	1	3	1	1	2	3	1	2	1	1.6 (0.84)
Luo et al.	2	2	2	1	1	3	1	3	1	1	1.7 (0.82)
Santana et al.	1	2	3	1	1	2	3	2	1	1	1.7 (0.82)
Felsky et al.	1	3	2	1	1	2	1	3	2	1	1.7 (0.82)
van Rooij et al.	1	2	2	2	1	2	2	3	2	1	1.8 (0.63)
King et al.	1	2	3	2	1	3	1	2	2	1	1.8 (0.79)
Humphries et al.	1	1	3	3	1	2	3	2	1	1	1.8 (0.92)
Guennewig et al.	1	2	2	2	1	2	2	3	2	2	1.9 (0.57)
Li et al.	2	2	3	1	1	2	2	3	1	2	1.9 (0.74)
Piras et al.	1	2	3	1	1	2	2	3	1	3	1.9 (0.88)
Magistry et al.	1	2	3	1	1	3	3	2	2	1	1.9 (0.88)
Fisher et al.	1	2	3	2	1	2	1	3	3	1	1.9 (0.88)
Annese et al.	1	1	3	2	1	2	3	2	1	3	1.9 (0.88)
Caldwell et al.	1	2	3	2	1	1	3	3	2	1	1.9 (0.88)
Das et al.	1	2	3	2	1	1	2	3	3	2	2 (0.82)
Panitch et al.	3	2	3	3	1	2	1	3	1	1	2 (0.94)
Miller et al.	2	2	2	2	1	2	2	3	3	2	2.1 (0.57)
Marques-Coelho et al.	3	2	3	2	2	2	2	3	2	2	2.3 (0.48)
Average score per criteria (standard deviation)	1.3 (0.62)	1.8 (0.53)	2.4 (0.77)	1.7 (0.64)	1.1 (0.34)	2 (0.55)	2 (0.83)	2.4 (0.71)	1.8 (0.68)	1.4 (0.65)	1.8 (0.75)