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VU Research Portal

Cracking the code-ing sequence for Parkinson’s disease

Jansen, I.E.

2017

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Jansen, I. E. (2017). Cracking the code-ing sequence for Parkinson’s disease.

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CHAPTER 3

Establishing the role of

rare coding variants in known

Parkinson’s disease risk loci

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3 ABSTRACT

Importance͗DĂŶǇĐŽŵŵŽŶŐĞŶĞƟĐĨĂĐƚŽƌƐŚĂǀĞďĞĞŶŝĚĞŶƟĮĞĚƚŽĐŽŶƚƌŝďƵƚĞƚŽ WƐƵƐĐĞƉƟďŝůŝƚǇ͕ŝŵƉƌŽǀŝŶŐŽƵƌƵŶĚĞƌƐƚĂŶĚŝŶŐŽĨƚŚĞƌĞůĂƚĞĚƵŶĚĞƌůǇŝŶŐďŝŽůŽŐŝĐĂů mechanisms. KďũĞĐƟǀĞ͗dŽĞǆƉůŽƌĞƚŚĞŝŶǀŽůǀĞŵĞŶƚŽĨƌĂƌĞŐĞŶĞƟĐǀĂƌŝĂŶƚƐŝŶĐŽŵŵŽŶƐƉŽƌĂĚŝĐ

risk loci for Parkinson’s disease.

ĞƐŝŐŶ͕ƐĞƫŶŐĂŶĚƉĂƌƟĐŝƉĂŶƚƐ͗hƐŝŶŐ/ŶƚĞƌŶĂƟŽŶĂůWĂƌŬŝŶƐŽŶ͛ƐŝƐĞĂƐĞ'ĞŶŽŵŝĐƐ

ŽŶƐŽƌƟƵŵ;/W'ͿĚĂƚĂƐĞƚƐ͕ǁĞƉĞƌĨŽƌŵĞĚĂĐŽŵƉƌĞŚĞŶƐŝǀĞƐƚƵĚǇƚŽĚĞƚĞƌŵŝŶĞ ƚŚĞ ŝŵƉĂĐƚ ŽĨ ƌĂƌĞ ǀĂƌŝĂŶƚƐ ŝŶ Ϯϲ ƉƌĞǀŝŽƵƐůǇ ƉƵďůŝƐŚĞĚ 't^ ůŽĐŝ ŝŶ W͘ dŚĞƐĞ ĚĂƚĂƐĞƚƐ ĞŶĐŽŵƉĂƐƐĞĚ ǁŚŽůĞͲĞǆŽŵĞ ƐĞƋƵĞŶĐŝŶŐ ĚĂƚĂ ŽĨ ϭ͕ϭϲϳ ĐĂƐĞƐ ĂŶĚ ϭ͕ϲϴϱ controls and a genotype-array NeuroX dataset, comprising 6,801 cases and 5,970 ĐŽŶƚƌŽůƐ͘tĞĂƉƉůŝĞĚWƌŝǆĮǆĞƚŽƐĞůĞĐƚƚŚĞƉƵƚĂƟǀĞĐĂƵƐĂůŐĞŶĞƐƵŶĚĞƌŶĞĂƚŚƚŚĞ 't^ƉĞĂŬƐ͕ǁŚŝĐŚǁĂƐďĂƐĞĚŽŶƵŶĚĞƌůǇŝŶŐĨƵŶĐƟŽŶĂůƐŝŵŝůĂƌŝƟĞƐ͘dŚĞ^ĞƋƵĞŶĐĞ <ĞƌŶĞůƐƐŽĐŝĂƟŽŶdĞƐƚ;^<dͿǁĂƐƵƐĞĚƚŽĂŶĂůǇǌĞƚŚĞũŽŝŶƚĞīĞĐƚŽĨƌĂƌĞ͕ĐŽŵŵŽŶ ŽƌďŽƚŚƚǇƉĞƐŽĨǀĂƌŝĂŶƚƐŽŶWƐƵƐĐĞƉƟďŝůŝƚǇ͘ůůŐĞŶĞƐǁĞƌĞƚĞƐƚĞĚƐŝŵƵůƚĂŶĞŽƵƐůǇ as a gene-set and each gene individually.

DĂŝŶŽƵƚĐŽŵĞĂŶĚŵĞĂƐƵƌĞƐ͗WŚĞŶŽƚǇƉŝĐŝŶĨŽƌŵĂƟŽŶǁĂƐĞǆƚƌĂĐƚĞĚĨƌŽŵĐůŝŶŝĐĂů

ŝŶĨŽƌŵĂƟŽŶŐĂƚŚĞƌĞĚďǇůŽĐĂůŝŶƐƟƚƵƚĞƐƉĂƌƟĐŝƉĂƟŶŐŝŶ/W'͘dŚĞŐĞŶĞƟĐĚĂƚĂ ĐŽŶƐŝƐƚƐŽĨǁŚŽůĞĞǆŽŵĞƐĞƋƵĞŶĐŝŶŐĂŶĚĂŐĞŶŽƚǇƉĞĂƌƌĂǇĞŶƌŝĐŚĞĚĨŽƌ;ŶĞƵƌŽůŽŐŝĐͿ rare coding variants.

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3 /EdZKhd/KE

'ĞŶĞƟĐ ĨĂĐƚŽƌƐ ƉůĂǇ ĂŶ ŝŵƉŽƌƚĂŶƚ ƌŽůĞ ŝŶ WĂƌŬŝŶƐŽŶ͛Ɛ ĚŝƐĞĂƐĞ ;WͿ ƉĂƚŚŽŐĞŶĞƐŝƐ͘ /Ŷ ĂĚĚŝƟŽŶƚŽƚŚĞĚŝƐĐŽǀĞƌǇŽĨƌĂƌĞǀĂƌŝĂŶƚƐƵƐŝŶŐĨĂŵŝůǇͲďĂƐĞĚůŝŶŬĂŐĞƐƚƵĚŝĞƐ͕ƌĞƐƵůƟŶŐŝŶ ƚŚĞŝĚĞŶƟĮĐĂƟŽŶŽĨĨŽƌĞǆĂŵƉůĞSNCA, LRRK2, parkin, DJ-1, PINK1 and VPS35, numerous ŐĞŶŽŵĞͲǁŝĚĞ ĂƐƐŽĐŝĂƟŽŶ ƐƚƵĚŝĞƐ ;'t^Ϳ ŚĂǀĞ ƐŚŽǁŶ ƚŚĂƚ ĐŽŵŵŽŶ ŐĞŶĞƟĐ ǀĂƌŝĂŶƚƐ increase PD risk.1_{dŚĞŵŽƐƚƌĞĐĞŶƚĂŶĚůĂƌŐĞƐƚWĂƐƐŽĐŝĂƟŽŶƐƚƵĚǇ}2_{ŝĚĞŶƟĮĞĚŽǀĞƌϮϬ} ĐŽŵŵŽŶƌŝƐŬǀĂƌŝĂŶƚƐ͕ĐŽŶĮƌŵŝŶŐŵĂŶǇƉƌĞǀŝŽƵƐůǇĂƐƐŽĐŝĂƚĞĚƌŝƐŬĨĂĐƚŽƌƐ͘ EĞǀĞƌƚŚĞůĞƐƐ͕ŚĞƌŝƚĂďŝůŝƚǇĞƐƟŵĂƚĞƐŝŶĚŝĐĂƚĞƚŚĂƚĂĚĚŝƟŽŶĂůŐĞŶĞƟĐƌŝƐŬĨĂĐƚŽƌƐ ƌĞŵĂŝŶ ƚŽ ďĞ ĚŝƐĐŽǀĞƌĞĚ ƐŝŶĐĞ Ă ƌĞůĂƟǀĞůǇ ůĂƌŐĞ ĨƌĂĐƟŽŶ ŽĨ W ŚĞƌŝƚĂďŝůŝƚǇ ĐĂŶŶŽƚ ďĞ ĞǆƉůĂŝŶĞĚďǇŬŶŽǁŶWƌŝƐŬůŽĐŝŽƌDĞŶĚĞůŝĂŶŐĞŶĞƐ͘3-5_{'t^ĂƉƉƌŽĂĐŚĞƐĂƌĞƉƌŝŵĂƌŝůǇ} ĚĞƐŝŐŶĞĚƚŽŝĚĞŶƟĨǇĐŽŵŵŽŶƌŝƐŬǀĂƌŝĂŶƚƐďǇƚŚĞƵƐĂŐĞŽĨŐĞŶŽƚǇƉŝŶŐĂƌƌĂǇƐ͘,ŽǁĞǀĞƌ͕ ĞŵĞƌŐŝŶŐĞǀŝĚĞŶĐĞƐƵŐŐĞƐƚƐƚŚĂƚƌĂƌĞǀĂƌŝĂŶƚƐŵĂǇĞǆƉůĂŝŶƉĂƌƚŽĨƚŚĞŵŝƐƐŝŶŐŚĞƌŝƚĂďŝůŝƚǇ͘6,7 ZĂƌĞǀĂƌŝĂŶƚƐŝŶƉƌŽƚĞŝŶĐŽĚŝŶŐƌĞŐŝŽŶƐĂƌĞŵŽƌĞůŝŬĞůǇƚŽĂīĞĐƚƚŚĞĨƵŶĐƟŽŶŽĨĂŐĞŶĞ than common variants which tag the causal variants via linkage disequilibrium (LD) and ĂƌĞŽŌĞŶůŽĐĂƚĞĚŝŶŶŽŶͲĐŽĚŝŶŐƌĞŐŝŽŶƐŽĨƚŚĞŐĞŶŽŵĞ͘8,9_{Therefore, rare variants might} ďĞ ŽĨ ŵŽƌĞ ŝŵƉŽƌƚĂŶĐĞ ƚŽ ĐŽŵƉůĞǆ ĚŝƐĞĂƐĞƐ ƚŚĂŶ ƉƌĞĚŝĐƚĞĚ ďǇ ƚŚĞ ŽŵŵŽŶ ŝƐĞĂƐĞͲ Common Variant hypothesis.10-13_{/Ŷ ĐŽŶƚƌĂƐƚ ƚŽ 't^͕ ĞǆŽŵĞ ƐĞƋƵĞŶĐŝŶŐ ƐƚƵĚŝĞƐ Ăŝŵ} ĂƚƐǇƐƚĞŵĂƟĐĂůůǇĂŶĂůǇǌŝŶŐĐŽĚŝŶŐ ƌĞŐŝŽŶƐ ŽĨƚŚĞŐĞŶŽŵĞƚŽŝĚĞŶƟĨǇĐĂƵƐĂů ǀĂƌŝĂŶƚƐŝŶ ĐŽŵƉůĞǆĚŝƐĞĂƐĞƐ͘14_{ǆŽŵĞƐƚƵĚŝĞƐŚĂǀĞďĞĞŶƉƌŽǀĞŶƚŽďĞĞīĞĐƟǀĞĨŽƌƐƚƵĚǇŝŶŐĨĂŵŝůŝĂů} disease15_{ďƵƚĂŶŝŶĐƌĞĂƐŝŶŐŶƵŵďĞƌŽĨĂƉƉůŝĐĂƟŽŶƐĨŽƌƉŽƉƵůĂƟŽŶƐͲďĂƐĞĚ ƐƚƵĚŝĞƐ ŚĂǀĞ} been developed.16,17

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3 Dd,K^

Subjects ůůWĐĂƐĞƐŝŶĐůƵĚĞĚŝŶƚŚŝƐƐƚƵĚǇŚĂǀĞŐŝǀĞŶǁƌŝƩĞŶŝŶĨŽƌŵĞĚĐŽŶƐĞŶƚ͘ZĞůĞǀĂŶƚůŽĐĂů ĞƚŚŝĐĂůĐŽŵŵŝƩĞĞƐĨŽƌŵĞĚŝĐĂůƌĞƐĞĂƌĐŚĂƉƉƌŽǀĞĚŝŶǀŽůǀĞŵĞŶƚŝŶŐĞŶĞƟĐƐƚƵĚŝĞƐ͘dŚĞW ƉĂƟĞŶƚƐǁĞƌĞĚŝĂŐŶŽƐĞĚƵƐŝŶŐƚŚĞh<ƌĂŝŶĂŶŬĐƌŝƚĞƌŝĂ͘26 tŚŽůĞĞǆŽŵĞƐĞƋƵĞŶĐŝŶŐĚĂƚĂƐĞƚ dŚĞǁŚŽůĞĞǆŽŵĞƐĞƋƵĞŶĐŝŶŐ;t^ͿĚĂƚĂƐĞƚŝŶĐůƵĚĞƐϭ͕ϭϲϳWĐĂƐĞƐĂŶĚϭ͕ϲϴϱĐŽŶƚƌŽůƐ ;ƉŽƐƚYͿŽĨƵƌŽƉĞĂŶĂŶĐĞƐƚƌǇ͘dŚĞWƉĂƟĞŶƚƐŚĂǀĞĂƚĞŶĚĞŶĐǇƚŽǁĂƌĚƐĂǇŽƵŶŐĂŐĞ of onset with an average of 41.2 years (SD = 10.9). 1,201 controls originate from the ZŽƩĞƌĚĂŵ^ƚƵĚǇǀĞƌƐŝŽŶϭ;Z^yϭͿ͕ĂƐǁĞŵĞƌŐĞĚƚŚĞ/W't^ĚĂƚĂǁŝƚŚƚŚĞZ^yϭt^ data.27_{dŚĞƐĂŵƉůĞƐǁĞƌĞƐĞƋƵĞŶĐĞĚŝŶĚŝīĞƌĞŶƚďĂƚĐŚĞƐǁŝƚŚƚǁŽĞǆŽŵĞĐĂƉƚƵƌĞŬŝƚƐ͗} ǆŽŵĞ>ŝďƌĂƌǇǀϮ͘Ϭ;ZŽĐŚĞͬEŝŵďůĞŐĞŶͿĂŶĚdƌƵƐĞƋǆŽŵĞŶƌŝĐŚŵĞŶƚ<ŝƚƚĂƌŐĞƟŶŐϰϰ͘ϭ DďĂŶĚϲϮDď͕ƌĞƐƉĞĐƟǀĞůǇ;^ƵƉƉůĞŵĞŶƚĂƌǇdĂďůĞϭͿ͘dŽĂĐĐŽƵŶƚĨŽƌƉƵƚĂƟǀĞƚĞĐŚŶŝĐĂů ĚŝīĞƌĞŶĐĞƐ ďĞƚǁĞĞŶ ƚŚĞ ĚŝīĞƌĞŶƚ ĐĂƉƚƵƌĞ ŬŝƚƐ͕ ǁĞ ŽŶůǇ ĐŽŶƐŝĚĞƌĞĚ ǀĂƌŝĂŶƚƐ ƚŚĂƚ ǁĞƌĞ targeted by both capture protocols and included preQC individual sample missingness (as ĂƌĞĨĞƌĞŶĐĞƚŽƐĞƋƵĞŶĐŝŶŐĐŽǀĞƌĂŐĞͿĂƐĐŽǀĂƌŝĂƚĞƐĚƵƌŝŶŐĂůůŐĞŶĞƟĐĂŶĂůǇƐĞƐ͘

KŶĂǀĞƌĂŐĞ͕ϵϰ͘ϰйŽĨƚŚĞĞǆŽŵĞǁĂƐĐŽǀĞƌĞĚĨŽƌĂƚůĞĂƐƚϭϬǆ͘dŚĞϭϬϬͲďƉƉĂŝƌĞĚͲ end reads were sequenced on a HiSeq2000 and aligned to the human reference genome (build hg19) using Barrow Wheeler Aligner (BWA)-MEM28_{͘ 'ĞŶŽŵĞ ŶĂůǇƐŝƐ dŽŽůŬŝƚ}29 ;'d<ͿĐĂůůĞĚƐŝŶŐůĞŶƵĐůĞŽƟĚĞǀĂƌŝĂŶƚƐ;^EsƐͿĂŶĚƐŵĂůůŝŶƐĞƌƟŽŶƐͬĚĞůĞƟŽŶƐ;ŝŶĚĞůƐͿĨŽƌ ĞĂĐŚƐĂŵƉůĞ͕ƌĞƐƵůƟŶŐŝŶŝŶĚŝǀŝĚƵĂůŐs&ĮůĞƐ͘'ĞŶŽƚǇƉĞƐŽĨĂůů/W'ĂŶĚZ^yϭĞǆŽŵĞ ƐĂŵƉůĞƐ ǁĞƌĞ ƚŚĞŶ ũŽŝŶƚůǇ ĐĂůůĞĚ ĂŶĚ ƌĞĐĂůŝďƌĂƚĞĚ͕ ĂůůŽǁŝŶŐ ƚŽ ŵĞƌŐĞ ƚŚĞ ĚŝƐƟŶĐƚ t^ ĚĂƚĂƐĞƚƐŝŶĂĐŽƌƌĞĐƚŵĂŶŶĞƌ͘^ƚĂŶĚĂƌĚ'd<ĮůƚĞƌƐƚĞƉƐǁĞƌĞĂƉƉůŝĞĚ͕ƚŽŐĞƚŚĞƌǁŝƚŚĂ minimum genotype quality Phred-score of 20 and depth of 8, to only select high-quality ǀĂƌŝĂŶƚƐ͘ KŶůǇ ďŝͲĂůůĞůŝĐ ĐĂůůƐ ǁĞƌĞ ĐŽŶƐŝĚĞƌĞĚ ƚŚĂƚ ǁĞƌĞ ůŽĐĂƚĞĚ ŝŶ ƌĞŐŝŽŶƐ ƚĂƌŐĞƚĞĚ ďǇ ďŽƚŚĐĂƉƚƵƌĞŬŝƚƐ͘^ƵƉƉůĞŵĞŶƚĂƌǇdĂďůĞϮƌĞƉŽƌƚƐƚŚĞĞǆŽŶƐƚŚĂƚŚĂǀĞďĞĞŶĞǆĐůƵĚĞĚĚƵĞ ƚŽŝŶƐƵĸĐŝĞŶƚĐŽǀĞƌĂŐĞǁŝƚŚŝŶŽŶĞŽĨƚŚĞĞǆŽŵĞĐĂƉƚƵƌĞƉƌŽƚŽĐŽůƐ͘

NeuroX dataset

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3

YƵĂůŝƚǇƉƌŽĐĞĚƵƌĞƐ

&Žƌ ŝŶĚŝǀŝĚƵĂů Y ŝŶ ďŽƚŚ ƚŚĞ t^ ĂŶĚ ƚŚĞ EĞƵƌŽy ĚĂƚĂƐĞƚƐ͕ ƐĂŵƉůĞƐ ǁĞƌĞ ƌĞŵŽǀĞĚ ǁŚĞŶ ƐŚŽǁŝŶŐ ŐĞŶĚĞƌ ĂŵďŝŐƵŝƚǇ͕ ĚƵďŝŽƵƐ ŚĞƚĞƌŽǌǇŐŽƐŝƚǇͬŐĞŶŽƚǇƉĞ ĐĂůůƐ͕ ĞǀŝĚĞŶĐĞ ŽĨ ƌĞůĂƚĞĚŶĞƐƐ͕ŽƌďĞŝŶŐĂƉŽƉƵůĂƟŽŶŽƵƚůŝĞƌ͘dŚĞůĂƩĞƌƚǁŽǁĞƌĞĐĂůĐƵůĂƚĞĚǁŝƚŚ>ͲƉƌƵŶĞĚ ĐŽŵŵŽŶ ǀĂƌŝĂŶƚƐ͘ sĂƌŝĂŶƚ Y ƉƌŽĐĞĚƵƌĞƐ ǁĞƌĞ ƐůŝŐŚƚůǇ ĚŝīĞƌĞŶƚ ĨŽƌ ƚŚĞ ƚǁŽ ĚŝīĞƌĞŶƚ ĚĂƚĂƐĞƚƐ͘&ŽƌƚŚĞt^ĚĂƚĂƐĞƚ͕ǀĂƌŝĂŶƚƐƉĂƐƐĞĚYǁŚĞŶŚĂǀŝŶŐĂŵŝŶŝŵƵŵĐĂůůƌĂƚĞх 85% and being in Hardy-Weinberg equilibrium (HWE pͲǀĂůƵĞƐхϭĞͲϴďĂƐĞĚŽŶĐŽŶƚƌŽůƐͿ͘ &ŽƌƚŚĞEĞƵƌŽyĚĂƚĂƐĞƚ͕ǀĂƌŝĂŶƚƐǁĞƌĞĞǆĐůƵĚĞĚĨŽƌƐƵďƐĞƋƵĞŶƚĂŶĂůǇƐĞƐǁŝƚŚĂŵŝŶŝŵƵŵ call rate < 95%, a HWE pͲǀĂůƵĞфϭĞͲϲ͕ŽƌǁŝƚŚƐŝŐŶŝĮĐĂŶƚĚŝīĞƌĞŶĐĞƐŝŶŵŝƐƐŝŶŐŶĞƐƐƌĂƚĞ between cases and controls.

ĂƵƐĂůŐĞŶĞƐĞůĞĐƟŽŶǁŝƚŚŝŶWƌŝƐŬůŽĐŝ

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ŽŵďŝŶĞĚ ŶŶŽƚĂƟŽŶ ĞƉĞŶĚĞŶƚ ĞƉůĞƟŽŶ ;Ϳ ǀϭ͘34_{&ŝŐƵƌĞ ϭ ĚŝƐƉůĂǇƐ Ă ǁŽƌŬŇŽǁ} ŽĨ ƚŚĞ ĐůĂƐƐŝĮĐĂƟŽŶ ŽĨ ƚŚĞ ĚŝīĞƌĞŶƚ ǀĂƌŝĂŶƚ ƐƵďƐĞƚƐ͘ dŚĞ ĞǆŽŶŝĐ ƐƵďƐĞƚ ǁĂƐ ĞǆĐůƵƐŝǀĞůǇ tested for the gene-set analysis to determine the involvement of common PD risk loci in ƚŚĞt^ĂŶĚEĞƵƌŽyĚĂƚĂƐĞƚ͘dŚĞ^ĞƋƵĞŶĐĞ<ĞƌŶĞůƐƐŽĐŝĂƟŽŶdĞƐƚ;^<dͿ35,36_{was used to} ƉĞƌĨŽƌŵďƵƌĚĞŶĂŶĂůǇƐĞƐ͘dŚĞD&ƚŚƌĞƐŚŽůĚ͕ƐĞƉĂƌĂƟŶŐƚŚĞƌĂƌĞĂŶĚĐŽŵŵŽŶǀĂƌŝĂŶƚƐ͕ ǁĂƐďĂƐĞĚŽŶƚŚĞƚŽƚĂůƐĂŵƉůĞƐŝǌĞƵƐŝŶŐƚŚĞĨŽƌŵƵůĂ;dсϭͬ;я;ϮŶͿͿͿƐƵŐŐĞƐƚĞĚďǇ^<d͕36

dĂďůĞϭ͘Selected set of genes

WŽůǇŵŽƌƉŚŝƐŵ >ŽĐĂƟŽŶ;ŚŐϭϵͿ PͲǀĂůƵĞ Seeding SNP WƌŝǆĮǆĞŐĞŶĞ rs71628662 chr1:155359992 ϲ͘ϴϲǆϭϬ-28 _NA rs823118 chr1:205723572 ϭ͘ϵϲǆϭϬ-16 _rs823114 _RAB7L1 rs10797576 chr1:232664611 ϭ͘ϳϲǆϭϬ-10 _rs2182431 _SIPA1L2 rs6430538 chr2:135539967 ϯ͘ϯϱǆϭϬ-19 _rs6430538 _ACMSD rs1955337 chr2:169129145 ϭ͘ϲϳǆϭϬ-20 _rs2390669 _STK39 rs12637471 chr3:182762437 ϱ͘ϯϴǆϭϬ-22 _rs12637471 _LAMP3 rs11724635 chr4:15737101 ϰ͘ϮϲǆϭϬ-17 _rs11724635 _&y>ϱ rs6812193 chr4:77198986 ϭ͘ϴϱǆϭϬ-11 _rs6812193 _STBD1 rs356182 chr4:90626111 ϭ͘ϴϱǆϭϬ-82 _rs356219 _SNCA rs34311866 chr4:951947 ϲ͘ϬǆϭϬ-41 _rs748483 _D&^ϳ rs9275326 chr6:32666660 ϱ͘ϴϭǆϭϬ-13 _rs9275311 _HLA-DRB5 rs199347 chr7:23293746 ϱ͘ϲϮǆϭϬ-14 _rs199347 _GPNMB rs591323 chr8:16697091 ϯ͘ϭϳǆϭϬ-8 _NA rs117896735 chr10:121536327 ϭ͘ϮϭǆϭϬ-11 _rs10886515 _RGS10 rs329648 chr11:133765367 ϴ͘ϬϱǆϭϬ-12 _rs329648 _SPATA19 rs3793947 chr11:83544472 Ϯ͘ϱϵǆϭϬ-08 _rs1400313 _DLG2 rs11060180 chr12:123303586 ϯ͘ϬϴǆϭϬ-11 _rs11060180 _HIP1R rs76904798 chr12:40614434 ϰ͘ϴϲǆϭϬ-14 _rs2708435 _LRRK2 rs7155501 chr14:55347827 ϭ͘ϮϱǆϭϬ-10 _rs2878174 _LGALS3 rs1555399 chr14:67984370 ϱ͘ϳϬǆϭϬ-16 _rs7155830 _ARG2 rs2414739 chr15:61994134 ϯ͘ϱϵǆϭϬ-12 _NA rs14235 chr16:31121793 ϯ͘ϲϯǆϭϬ-12 _rs14235 _PRSS8 rs17649553 chr17:43994648 ϲ͘ϭϭǆϭϬ-49 _rs17649553 _MAPT rs12456492 chr18:40673380 Ϯ͘ϭϱǆϭϬ-11 _rs12456492 _RIT2 rs62120679 chr19:2363319 Ϯ͘ϱϮǆϭϬ-09 _rs2074546 _PLEKHJ1 rs55785911 chr20:3153503 ϯ͘ϯϬǆϭϬ-10 _rs2295545 _AVP

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dŽ ĐŽƌƌĞĐƚ ĨŽƌ ĐŽŶĨŽƵŶĚŝŶŐ ĨĂĐƚŽƌƐ ;Ğ͘Ő͘ ƉŽƉƵůĂƟŽŶ ƐƚƌĂƟĮĐĂƟŽŶ ĂŶĚ ƚĞĐŚŶŝĐĂů ĂƌƟĨĂĐƚƐͿ͕ǁĞŝŶĐůƵĚĞĚϮϬŵƵůƟͲĚŝŵĞŶƐŝŽŶĂůƐĐĂůŝŶŐĐŽŵƉŽŶĞŶƚƐ͕ŐĞŶĚĞƌĂŶĚŝŶĚŝǀŝĚƵĂů missingness rate pre QC (as a reference to the individual WES coverage) for the WES ĚĂƚĂƐĞƚ͘ƐƚŚĞEĞƵƌŽyĚĂƚĂƐĞƚŝƐŵŽƌĞŚŽŵŽŐĞŶĞŽƵƐ͕ǁĞĐŽƌƌĞĐƚĞĚĨŽƌƚŚĞĮƌƐƚϰD^ components and gender. Empirical pͲǀĂůƵĞƐǁĞƌĞĐĂůĐƵůĂƚĞĚĨŽƌƐŝŐŶŝĮĐĂŶƚƐĂŵƉůĞƌĞƐƵůƚƐ (pфϬ͘ϬϱͿ͘&ŽƌƚŚĞŐĞŶĞͲƐĞƚĂŶĂůǇƐŝƐ͕ƚŚĞŽƌŝŐŝŶĂůƐĂŵƉůĞp-value of the gene-set of interest was compared to pͲǀĂůƵĞƐŽĨϭ͕ϬϬϬƌĂŶĚŽŵůǇĚƌĂǁŶŐĞŶĞͲƐĞƚƐŽĨƚŚĞƐĂŵĞƐŝǌĞ͘&ŽƌƚŚĞ ŝŶĚŝǀŝĚƵĂů ŐĞŶĞ ĂƐƐŽĐŝĂƟŽŶƐ͕ ĞŵƉŝƌŝĐĂů p-values were calculated using the resampling ŵĞƚŚŽĚŝŵƉůĞŵĞŶƚĞĚďǇ^<d͕ďǇϭϬ͕ϬϬϬƉĞƌŵƵƚĂƟŽŶƐŽĨƚŚĞĂīĞĐƟŽŶƐƚĂƚƵƐ͘ŵƉŝƌŝĐĂů

p-values are calculated by (n1+1)/(n+1), where n1 = the number of resampling p-values

smaller than the original sample p-value and n = the number of resampling.

WŽǁĞƌĐĂůĐƵůĂƟŽŶƐ tĞ ĞƐƟŵĂƚĞĚ ƚŚĞ ƉŽǁĞƌ ŽĨ ŽƵƌ ƐƚƵĚǇ ĚĞƐŝŐŶ ƚŽ ĚĞƚĞĐƚ ƌĂƌĞ ǀĂƌŝĂŶƚ ĂƐƐŽĐŝĂƟŽŶƐ͘ ^ƵƉƉůĞŵĞŶƚĂƌǇ dĂďůĞ ϯ ĚŝƐƉůĂǇƐ ƚŚĞ ƉĂƌĂŵĞƚĞƌƐ ƚŚĂƚ ǁĞƌĞĐŚŽƐĞŶ ĨŽƌ ƚŚĞ ĐĂůĐƵůĂƟŽŶƐ͘ &ŽƌďŽƚŚĚĂƚĂƐĞƚƐ͕ƚŚĞWƉƌĞǀĂůĞŶĐĞǁĂƐƐĞƚƚŽϬ͘ϬϬϱϳ38_{͘ƐĂƉƉƌŽǆŝŵĂƚĞůǇŚĂůĨŽĨƚŚĞ} ůŽĐŝŝŶWŐĞŶĞ͘ŽƌŐŚĂǀĞĂŶŽĚĚƐƌĂƟŽďĞůŽǁϭ͕ƚŚĞƉĞƌĐĞŶƚĂŐĞƉƌŽƚĞĐƟǀĞĞīĞĐƚǁĂƐƐĞƚ ƚŽϱϬй͘ƚŚŽƵƐĂŶĚƐŝŵƵůĂƟŽŶƐ;ɲсϬ͘ϬϮϱͿǁĞƌĞƉĞƌĨŽƌŵĞĚŽŶĂŚĂƉůŽƚǇƉĞŵĂƚƌŝǆŽĨ ^<d͕ŵŝŵŝĐŬŝŶŐůŝŶŬĂŐĞĚŝƐĞƋƵŝůŝďƌŝƵŵƐƚƌƵĐƚƵƌĞŽĨƵƌŽƉĞĂŶĂŶĐĞƐƚƌǇ͕ĐŽŵƉƌŝƐŝŶŐϭϬ͕ϬϬϬ haplotypes over 200 kb regions.

Z^h>d^

t^ĂŶĚƌĂƌĞǀĂƌŝĂŶƚƐ

&ŝƌƐƚ͕ǁĞĂŶĂůǇǌĞĚƚŚĞt^ĚĂƚĂƐĞƚĂƐŝƚƌĞƉƌĞƐĞŶƚƐĂůůĞǆŽŶŝĐǀĂƌŝĂŶƚƐ͕ŽĨǁŚŝĐŚƚŚĞƐƚƵĚǇ ĚĞƐŝŐŶŚĂƐϲϱйƉŽǁĞƌƚŽĚĞƚĞĐƚĂƌĂƌĞǀĂƌŝĂŶƚĂƐƐŽĐŝĂƟŽŶƐŝŐŶĂůĐŽŶƐŝĚĞƌŝŶŐŝŶĚŝǀŝĚƵĂů ŐĞŶĞƐ͘dĞƐƟŶŐƚŚĞĂŐŐƌĞŐĂƚĞĚĞīĞĐƚŽĨŐƌŽƵƉĞĚǀĂƌŝĂŶƚƐǁŝƚŚŝŶĂŐĞŶĞͲƐĞƚŚĂƐƚŚĞƉŽƚĞŶƟĂů to increase power. Supplementary Table 4 shows the results of the gene-set analyses in ƚŚĞt^ĚĂƚĂƐĞƚ͘ŽŵŵŽŶĞǆŽŶŝĐǀĂƌŝĂŶƚƐĂƌĞŵŽĚĞƌĂƚĞůǇĂƐƐŽĐŝĂƚĞĚƚŽW͘dŚĞŶŽŵŝŶĂů p-ǀĂůƵĞŝƐƐŝŐŶŝĮĐĂŶƚ͕ďƵƚƚŚĞĞŵƉŝƌŝĐĂů p-ǀĂůƵĞĞǆĐĞĞĚƐϬ͘Ϭϱ͘ůƚŚŽƵŐŚǁĞĂŶƟĐŝƉĂƚĞĚ Ă ƐŝŐŶŝĮĐĂŶƚ ĂƐƐŽĐŝĂƟŽŶ ŽĨ ĐŽŵŵŽŶ ǀĂƌŝĂŶƚƐ͕ ǁĞ ĂƩƌŝďƵƚĞ ƚŚĞ ŵŽĚĞƌĂƚĞ ĂƐƐŽĐŝĂƟŽŶ ƚŽ Ă ƌĞůĂƟǀĞůǇ ůŽǁ ƐĂŵƉůĞ ƐŝǌĞ ;ĐŽŵƉĂƌĞĚ ƚŽ ƚŚĞ ŽƌŝŐŝŶĂů 't^Ϳ͕ ĂŶĚ ƚŚĞ ƐĞůĞĐƟŽŶ ŽĨ ŐĞŶĞƐ;ďǇWƌŝǆĮǆĞͿǁŝƚŚǀĂƌŝĂŶƚƐŝŶŵŽĚĞƌĂƚĞ>ǁŝƚŚƚŚĞŽƌŝŐŝŶĂůŚŝŐŚĞƐƚ^EW͘dŚĞŐĞŶĞͲ ƐĞƚĂƐƐŽĐŝĂƟŽŶŝƐĂďƐĞŶƚǁŚĞŶĨŽĐƵƐŝŶŐŽŶƚŚĞĐŽŵŵŽŶĂŵŝŶŽĂĐŝĚĐŚĂŶŐŝŶŐĂŶĚ variants, which is probably due to a decrease in power as the number of variants drops.

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ŐĞŶĞƐƉĞƌǀĂƌŝĂŶƚƐƵďƐĞƚ͘&ŽƌƚŚĞǀĂƌŝĂŶƚƐ͕ŶŽŐĞŶĞŝƐŝŶĚĞƉĞŶĚĞŶƚůǇĂƐƐŽĐŝĂƚĞĚƚŽ W͘,ŽǁĞǀĞƌ͕ŝŶǀĞƐƟŐĂƟŶŐƚŚĞĂŵŝŶŽͲĂĐŝĚĐŚĂŶŐŝŶŐǀĂƌŝĂŶƚƐƵďƐĞƚƌĞƐƵůƚĞĚŝŶĂƐŝŐŶŝĮĐĂŶƚ ĂƐƐŽĐŝĂƟŽŶĨŽƌSTBD1 (empirical p = 0.046).

NeuroX and rare variants

dŚĞ EĞƵƌŽy ĚĂƚĂƐĞƚ ĐŽŶƚĂŝŶƐ ƉƌĞǀŝŽƵƐůǇ ŝĚĞŶƟĮĞĚ ĞǆŽŶŝĐ ǀĂƌŝĂŶƚƐ͕ ŽĨ ǁŚŝĐŚ Ă ůĂƌŐĞ ƉƌŽƉŽƌƟŽŶ ŝƐ ƌĂƌĞ͘30_{dŚĞ ůĂƌŐĞƌ ƐĂŵƉůĞ ƐŝǌĞ ;ϲ͕ϴϬϭ ĐĂƐĞƐ ĂŶĚ ϱ͕ϵϳϬ ĐŽŶƚƌŽůƐͿ ŝŶĐƌĞĂƐĞƐ} ƚŚĞƉŽǁĞƌ;ĞƐƟŵĂƚĞĚĂƚϵϲйͿƚŽĚĞƚĞĐƚĂƌĂƌĞǀĂƌŝĂŶƚĂƐƐŽĐŝĂƟŽŶƐŝŐŶĂů͘^ŝŵŝůĂƌůǇƚŽƚŚĞ t^ĚĂƚĂƐĞƚ͕ĂŵŽĚĞƌĂƚĞĐŽŵŵŽŶǀĂƌŝĂŶƚĂƐƐŽĐŝĂƟŽŶŝƐĚĞƚĞĐƚĞĚ;ŶŽŵŝŶĂůp = 0.031). /ŶĐŽŶƚƌĂƐƚƚŽƚŚĞt^ĚĂƚĂƐĞƚ͕ǁĞĚŽŽďƐĞƌǀĞƐŝŐŶŝĮĐĂŶƚĂƐƐŽĐŝĂƟŽŶƐŽĨƚŚĞŐĞŶĞͲƐĞƚ ǁŝƚŚW͕ĞǀĞŶǁŚĞŶŽŶůǇĐŽŶƐŝĚĞƌŝŶŐƌĂƌĞǀĂƌŝĂŶƚƐ;ĐŚĂŶŐŝŶŐсϬ͘ϬϬϳ͖сϬ͘ϬϬϮ͖ Supplementary Table 5a).

dŽĚŝƐĐŽǀĞƌǁŚĞƚŚĞƌƐƉĞĐŝĮĐŐĞŶĞƐĚƌŝǀĞƚŚŝƐŽďƐĞƌǀĞĚƌĂƌĞǀĂƌŝĂŶƚĂƐƐŽĐŝĂƟŽŶ ĚĞƚĞĐƚĞĚǁŝƚŚƚŚĞƚǁŽͲƐŝĚĞĚ^<dƚĞƐƚ͕ƚŚĞǀĂƌŝĂŶƚƐǁĞƌĞŐƌŽƵƉĞĚƉĞƌŐĞŶĞĂŶĚĂŐĂŝŶ ƚǁŽͲƐŝĚĞĚƚĞƐƚĞĚĨŽƌƚŚĞŝƌĂƐƐŽĐŝĂƟŽŶƚŽW͘LRRK2 ŝƐƚŚĞŐĞŶĞĚƌŝǀŝŶŐƚŚĞĂƐƐŽĐŝĂƟŽŶ ŽďƐĞƌǀĞĚŝŶƚŚĞƚŽƚĂůŐĞŶĞͲƐĞƚ;^ƵƉƉůĞŵĞŶƚĂƌǇdĂďůĞϲͿ͘&ŽĐƵƐŝŶŐŽŶƚŚĞƐƵďƐĞƚ͕ ƚŚŝƐĂƐƐŽĐŝĂƟŽŶ;ŶŽŵŝŶĂůp сϱ͘ϭϳǆϭϬ-13_{) is considerably stronger than the second most} ƐŝŐŶŝĮĐĂŶƚŐĞŶĞ͗SPATA19 (nominal p сϬ͘ϬϱϬͿ͘ƐƚŚĞEĞƵƌŽyĂƌƌĂǇŝƐŶĞƵƌŽůŽŐǇƐƉĞĐŝĮĐ͕ŝƚ harbors many variants of the known PD gene LRRK2͘&ƵƌƚŚĞƌŵŽƌĞ͕LRRK2 is a large gene coding for 2,527 amino acids. As a comparison, NeuroX contains 32 harmful (predicted by CADD) LRRK2 variants, while only 2 harmful variants are present for SPATA19. The variants in LRRK2 are overrepresented and biasing the results of the total gene-sets. We therefore ƉĞƌĨŽƌŵĞĚƚŚĞƐĂŵĞŐĞŶĞͲƐĞƚĂŶĂůǇƐĞƐŽŶƚŚĞEĞƵƌŽyĚĂƚĂƐĞƚĞǆĐůƵĚŝŶŐƚŚĞǀĂƌŝĂŶƚƐŽĨ

LRRK2;^ƵƉƉůĞŵĞŶƚĂƌǇdĂďůĞϱďͿ͕ƌĞƐƵůƟŶŐŝŶƚŚĞĂďƐĞŶĐĞŽĨĂƌĂƌĞǀĂƌŝĂŶƚĂƐƐŽĐŝĂƟŽŶ

in the NeuroX dataset (nominal p ш Ϭ͘ϮϴͿ͘ dŚŝƐ ƐƵŐŐĞƐƚƐ ƚŚĂƚ ƚŚĞ ƉƌĞǀŝŽƵƐůǇ ŽďƐĞƌǀĞĚ ĂƐƐŽĐŝĂƟŽŶŽĨƌĂƌĞǀĂƌŝĂŶƚƐǁŝƚŚŝŶƚŚĞƚŽƚĂůŐĞŶĞͲƐĞƚƚŽWǁĂƐƐŽůĞůǇĚƌŝǀĞŶďǇLRRK2.

dŚĞƚǁŽͲƐŝĚĞĚ^<dĂŶĂůǇƐŝƐƉĞƌŐĞŶĞĂŝŵĞĚĂƚƚŚĞĚŝƐĐŽǀĞƌǇŽĨŐĞŶĞƐĚƌŝǀŝŶŐ ƚŚĞƌĂƌĞǀĂƌŝĂŶƚĂƐƐŽĐŝĂƟŽŶŝŶƚŚĞƚŽƚĂůŐĞŶĞͲƐĞƚ͘EĞǆƚ͕ǁĞǁĞƌĞŝŶƚĞƌĞƐƚĞĚƚŽĞǆƉůŽƌĞƚŚĞ

dĂďůĞϮ͘'ĞŶĞͲďĂƐĞĚƌĂƌĞǀĂƌŝĂŶƚĂƐƐŽĐŝĂƟŽŶƌĞƐƵůƚƐĨŽƌt^ĚĂƚĂƐĞƚ͘

sĂƌŝĂŶƚƚǇƉĞ Gene pͲǀĂůƵĞ;ĞŵƉͿ n variants maf cases ŵĂĨĐŽŶƚƌŽůƐ

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ŐĞŶĞƟĐďƵƌĚĞŶŽĨƌĂƌĞǀĂƌŝĂŶƚƐĨŽƌĞĂĐŚŐĞŶĞŝŶĚŝǀŝĚƵĂůůǇǁŚĞŶĂƐƐƵŵŝŶŐĂůůƌĂƌĞǀĂƌŝĂŶƚƐ ƚŽŚĂǀĞƚŚĞƐĂŵĞĚŝƌĞĐƟŽŶŽĨĞīĞĐƚ;ŽŶĞͲƐŝĚĞĚhZEƚĞƐƚͿ͘dĂďůĞϯƐŚŽǁƐĂŐĂŝŶƚŚĂƚ

LRRK2 (empirical p с Ϭ͘ϬϬϬϱͿ ŝƐ ƚŚĞ ƐƚƌŽŶŐĞƐƚ ĂƐƐŽĐŝĂƚĞĚ ŐĞŶĞ͘ &ƵƌƚŚĞƌŵŽƌĞ͕ SPATA19

(empirical p сϬ͘ϬϭϳͿŝƐƐŝŐŶŝĮĐĂŶƚůǇĂƐƐŽĐŝĂƚĞĚǁŚĞŶƐƉĞĐŝĮĐĂůůǇĐŽŶƐŝĚĞƌŝŶŐƌĂƌĞ variants.

dĂďůĞϯ͘'ĞŶĞͲďĂƐĞĚƌĂƌĞǀĂƌŝĂŶƚĂƐƐŽĐŝĂƟŽŶƌĞƐƵůƚƐĨŽƌEĞƵƌŽyĚĂƚĂƐĞƚ͘

sĂƌŝĂŶƚƚǇƉĞ Gene pͲǀĂůƵĞ;ĞŵƉͿ n variants maf cases ŵĂĨĐŽŶƚƌŽůƐ

AAchanging LRRK2 Ϭ͘ϬϬϬϰ;Ϭ͘ϬϬϬϱͿ 48 1.70% 1.13% RIT2 0.051 2 0.00% 0.03% PRSS8 0.098 1 0.04% 0.01% CADD LRRK2 Ϭ͘ϬϬϬϯ;Ϭ͘ϬϬϬϱͿ 32 1.38% 0.86% SPATA19 Ϭ͘Ϭϭϰ;Ϭ͘ϬϭϳͿ 2 0.05% 0.00% RIT2 0.051 2 0.00% 0.03% p-value = nominal pͲǀĂůƵĞ͖;ĞŵƉ͘ͿсĞŵƉŝƌŝĐĂůpͲǀĂůƵĞĐĂůĐƵůĂƚĞĚďǇĐŽŵƉĂƌŝƐŽŶƚŽϭϬ͕ϬϬϬƉĞƌŵƵƚĂƟŽŶƐŽĨĂīĞĐƟŽŶƐƚĂƚƵƐ͘ ĐŚĂŶŐŝŶŐсĂŵŝŶŽĂĐŝĚĐŚĂŶŐŝŶŐǀĂƌŝĂŶƚƐ͖сǀĂƌŝĂŶƚƐƉƌĞĚŝĐƚĞĚƉĂƚŚŽŐĞŶŝĐ ŝƌĞĐƟŽŶĂůŝƚǇŽĨĞīĞĐƚ tĞĨƵƌƚŚĞƌĞǆƉůŽƌĞĚƚŚĞƐŝŐŶŝĮĐĂŶƚŝŶĚŝǀŝĚƵĂůĂƐƐŽĐŝĂƟŽŶƐŝŐŶĂůƐ;ĞŵƉŝƌŝĐĂůp < 0.05) for

LRRK2, STBD1, and SPATA19. By focusing on the variant level we aimed to comprehend the

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frequency of 6.2% in cases and 6.9% in controls. All 3 variants were detected in the WES ĚĂƚĂƐĞƚ͕ĂůůŽǁŝŶŐƚŽƚĞƐƚƚŚĞĨƵůůŚĂƉůŽƚǇƉĞ;'ͲͲͿ͘ůƚŚŽƵŐŚƚŚĞŚĂƉůŽƚǇƉĞĂƐƐŽĐŝĂƟŽŶ ǁĂƐŶŽƚƐŝŐŶŝĮĐĂŶƚŝŶƚŚĞt^ĚĂƚĂƐĞƚ;KZсϬ͘ϴϭ͕p Ϭ͘ϮϮϯͿ͕ƚŚĞƚƌĞŶĚŽĨĞīĞĐƚŝƐƐŝŵŝůĂƌǁŝƚŚ a minor haplotype frequency of 7.0% in cases and 7.5% in controls. The smaller sample ƐŝǌĞŽĨƚŚĞt^ĚĂƚĂƐĞƚŝƐĂƉůĂƵƐŝďůĞƌĞĂƐŽŶĨŽƌŶŽƚŽďƚĂŝŶŝŶŐĂƐŝŐŶŝĮĐĂŶƚĂƐƐŽĐŝĂƟŽŶ͘

EĞǆƚ͕ ƚŚĞ t^ͲďĂƐĞĚ STBD1 and NeuroX-based SPATA19 ǁĞƌĞ ŝŶǀĞƐƟŐĂƚĞĚ ĨŽƌ ƚŚĞŝƌ ǀĂƌŝĂŶƚ ĨƌĞƋƵĞŶĐŝĞƐ͘ ^ŝŶŐůĞͲŵĂƌŬĞƌ ĂƐƐŽĐŝĂƟŽŶ ĂŶĂůǇƐŝƐ ƐŚŽǁĞĚ ŶŽ ƐŝŐŶŝĮĐĂŶƚ individual results for the 8 variants within STBD1. It therefore appears that the observed ƌĂƌĞ ǀĂƌŝĂŶƚ ĂƐƐŽĐŝĂƟŽŶ ŝƐ ŶŽƚ ĐĂƵƐĞĚ ďǇ ŽŶĞ ĞǆĐůƵƐŝǀĞ ǀĂƌŝĂŶƚ ďƵƚ ŝƐ ƌĂƚŚĞƌ ƚŚĞ ĞīĞĐƚ ŽĨ ŵƵůƟƉůĞ ƌĂƌĞ ǀĂƌŝĂŶƚƐ͘ ^ĞǀĞŶ ŽĨ ƚŚĞ ϴ ǀĂƌŝĂŶƚƐ ĂƌĞ ĐŽŶƚƌŽůͲƐƉĞĐŝĮĐ ĂƐ ƚŚĞǇ ĂƌĞ ŽŶůǇ present in 10 control individuals. In contrast, only 1 variant is present in a single case. dŚĞĚŝƌĞĐƟŽŶŽĨĞīĞĐƚŽĨƚŚĞǀĂƌŝĂŶƚƐƚŚĂƚĂƌĞŐĞŶĞƌĂƟŶŐƚŚĞSTBD1 ŐĞŶĞĂƐƐŽĐŝĂƟŽŶŝƐ ƚŚĞƌĞĨŽƌĞŝŵƉůŝĞĚƚŽďĞƉƌŽƚĞĐƟǀĞ͘dŚĞƐŝŐŶŝĮĐĂŶƚŐĞŶĞͲďĂƐĞĚĂƐƐŽĐŝĂƟŽŶĨŽƌSPATA19 is ƌĞůĂƟǀĞůǇƐƚƌŽŶŐĐŽŶƐŝĚĞƌŝŶŐƚŚĂƚŝƚŝƐĚƌŝǀĞŶďǇŽŶůǇϮǀĂƌŝĂŶƚƐƚŚĂƚĂƌĞƉƌĞƐĞŶƚŝŶϳ cases and 0 controls. The absence of SPATA19 CADD variants in controls suggests that the ĂƐƐŽĐŝĂƟŽŶƐŝŐŶĂůŝƐĚĂŵĂŐŝŶŐ͘,ŽǁĞǀĞƌ͕SPATA19 variants could have been missed as the NeuroX dataset is array-based.

/^h^^/KE

dŽ ĞƐƚĂďůŝƐŚ ƚŚĞ ŝŶŇƵĞŶĐĞ ŽĨ ƌĂƌĞ ǀĂƌŝĂŶƚƐ ŝŶ ƐƉŽƌĂĚŝĐ W ƌŝƐŬ ůŽĐŝ͕ ǁĞ ĞǆƉůŽƌĞĚ ƚǁŽ independent PD datasets (WES and NeuroX) enriched for coding rare variants. We used ƚŚĞWƌŝǆ&ŝǆĞƐƚƌĂƚĞŐǇƚŽƐĞůĞĐƚƚŚĞŵŽƐƚůŝŬĞůǇĐĂƵƐĂůŐĞŶĞƐƵŶĚĞƌůǇŝŶŐƚŚĞWůŽĐŝƉĞĂŬƐ͕ ǁŚŝĐŚŝƐďĂƐĞĚŽŶŽǀĞƌůĂƉƉŝŶŐďŝŽůŽŐŝĐĂůĨƵŶĐƟŽŶĂůƐŝŵŝůĂƌŝƟĞƐ͘tĞƚĞƐƚĞĚďŽƚŚƚŚĞĞīĞĐƚ ŽĨƌĂƌĞǀĂƌŝĂŶƚƐŝŶƚŚĞŐĞŶĞͲƐĞƚĂƚŽŶĐĞ͕ĂƐĞĂĐŚŐĞŶĞŝŶĚŝǀŝĚƵĂůůǇ͘ŐŐƌĞŐĂƟŶŐǀĂƌŝĂŶƚƐ ƐŝŵƵůƚĂŶĞŽƵƐůǇĂĐƌŽƐƐĂƐĞƚŽĨŐĞŶĞƐŚĂƐƚŚĞƉŽƚĞŶƟĂůƚŽŝŶĐƌĞĂƐĞƉŽǁĞƌƚŽĚĞƚĞĐƚĂŶ ĂƐƐŽĐŝĂƟŽŶƐŝŐŶĂů͕ŐŝǀĞŶƚŚĂƚƚŚĞƐĞůĞĐƚĞĚŐĞŶĞƐĂƌĞĞŶƌŝĐŚĞĚĨŽƌĂŐƌŽƵƉŽĨŐĞŶĞƐƚŚĂƚĂƌĞ genuinely involved in the disease pathogenesis.

dŚĞĂǀĞƌĂŐĞĂŐĞŽĨŽŶƐĞƚǁŝƚŚŝŶƚŚĞĐĂƐĞŐƌŽƵƉŽĨƚŚĞt^ĚĂƚĂƐĞƚ;ΕϰϭǇĞĂƌƐͿ ŝƐϮϬǇĞĂƌƐǇŽƵŶŐĞƌƚŚĂŶŝŶƚŚĞŵĞƚĂͲĂŶĂůǇƐŝƐŽĨƚŚĞŵŽƐƚƌĞĐĞŶƚW't^;ΕϲϭǇĞĂƌƐͿ ǁŚĞƌĞƚŚĞWƌŝƐŬůŽĐŝǁĞƌĞďĂƐĞĚŽŶ͘ƐƐŽŵĞƌĂƌĞŐĞŶĞƟĐƌŝƐŬĨĂĐƚŽƌƐ;DJ-1, parkin and PINK1)1_{ĂƌĞƐƉĞĐŝĮĐĨŽƌǇŽƵŶŐŽŶƐĞƚW;zKWͿ͕ǁĞĂĐŬŶŽǁůĞĚŐĞƚŚĞƉƵƚĂƟǀĞĞǆŝƐƚĞŶĐĞŽĨ} zKWͲƐƉĞĐŝĮĐĐŽŵŵŽŶŐĞŶĞƟĐƌŝƐŬĨĂĐƚŽƌƐǁŝƚŚŝŶƚŚĞt^ĚĂƚĂƐĞƚ͘,ŽǁĞǀĞƌ͕ƌŝƐŬĨĂĐƚŽƌƐ ƌĞůĂƚĞĚ ƚŽ ůĂƚĞ ŽŶƐĞƚ ƐƉŽƌĂĚŝĐ W ŵŝŐŚƚ ĂůƐŽ ƉůĂǇ Ă ƌŽůĞ ŝŶ zKW͘ W ƌŝƐŬ ůŽĐŝ͕ ƐƵĐŚ ĂƐ

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ŝŶŇƵĞŶĐĞĚ ďǇ ƌĂƌĞ ǀĂƌŝĂŶƚƐ͕ ƉŽƐƐŝďůǇ ŝŶĐƌĞĂƐŝŶŐ ƚŚĞ ůŝŬĞůŝŚŽŽĚ ŽĨ ĚĞƚĞĐƟŶŐ ƌĂƌĞ ǀĂƌŝĂŶƚ ĂƐƐŽĐŝĂƟŽŶƐ͘

hƐŝŶŐŐĞŶĞͲƐĞƚĂƉƉƌŽĂĐŚŝŶƚŚĞt^ĚĂƚĂƐĞƚ͕ǁĞĚŝĚŶŽƚĚĞƚĞĐƚĂďƵƌĚĞŶŽĨƌĂƌĞ variants when comparing PD subjects to controls. However, it remains unclear whether ƚŚĞĂďƐĞŶĐĞŽĨĂƐƐŽĐŝĂƟŽŶŝƐŐĞŶƵŝŶĞŽƌĚƵĞƚŽŝŶƐƵĸĐŝĞŶƚƉŽǁĞƌŽƌŝŶĐŽƌƌĞĐƚƐĞůĞĐƟŽŶ ŽĨĐĂƵƐĂůŐĞŶĞƐ͘/ŶĐŽŶƚƌĂƐƚ͕ǁŝƚŚƚŚĞŐĞŶĞďĂƐĞĚĂƐƐŽĐŝĂƟŽŶƚĞƐƚĨŽƌƚŚĞŐĞŶĞƐƐĞůĞĐƚĞĚ ǁŝƚŚƚŚĞWƌŝǆĮǆĞƐƚƌĂƚĞŐǇǁĞŽďƐĞƌǀĞĚĂƌĂƌĞǀĂƌŝĂŶƚĂƐƐŽĐŝĂƟŽŶĨŽƌSTBD1, implying that rare variants in this gene could be a risk factor for PD. STBD1ŚĂƐŝƚƐĨƵŶĐƟŽŶŝŶůǇƐŽƐŽŵĂůͲ mediated autophagy that has been shown to contribute to PD pathogenesis.41_'ĞŶĞƟĐ ƌĞƉůŝĐĂƟŽŶŽƌĨƵŶĐƟŽŶĂůǀĂůŝĚĂƟŽŶĨŽƌSTBD1 is required. tĞ ĚĞƚĞĐƚĞĚ ƐƚƌŽŶŐ ĂƐƐŽĐŝĂƟŽŶƐ ŽĨ ƌĂƌĞ ǀĂƌŝĂŶƚƐ ǁŝƚŚŝŶ ƚŚĞ ŐĞŶĞͲƐĞƚ ĨŽƌ ƚŚĞ EĞƵƌŽy ĚĂƚĂƐĞƚ͘ ,ŽǁĞǀĞƌ͕ ƐƵďƐĞƋƵĞŶƚ ĂŶĂůǇƐĞƐ ƐŚŽǁĞĚ ƚŚĂƚ ƚŚĞƐĞ ĂƐƐŽĐŝĂƟŽŶƐ ǁĞƌĞ dominated by LRRK2 ǀĂƌŝĂŶƚƐ͘ƐƐŽĐŝĂƟŽŶĂŶĂůǇƐŝƐŽŶǀĂƌŝĂŶƚůĞǀĞůƌĞǀĞĂůĞĚƚŚĂƚƚŚĞLRRK2 ŐĞŶĞƐŝŐŶĂůǁĂƐĚƌŝǀĞŶďǇƚŚĞŬŶŽǁŶƉ͘'ϮϬϭϵ^ǀĂƌŝĂŶƚ͘dŚŝƐŽďƐĞƌǀĂƟŽŶŚŝŐŚůŝŐŚƚƐƚŚĞ ŝŵƉŽƌƚĂŶĐĞĨŽƌĞǀĞƌǇĂŐŐƌĞŐĂƚĞĚǀĂƌŝĂŶƚƐƚƵĚǇƚŽĨƵƌƚŚĞƌŝŶǀĞƐƟŐĂƚĞǀĂƌŝĂŶƚĂŐŐƌĞŐĂƟŽŶ ĂƐƐŽĐŝĂƟŽŶ ƌĞƐƵůƚƐ ŽŶ ǀĂƌŝĂŶƚ ůĞǀĞů ƚŽ ĐŽƌƌĞĐƚůǇ ĚƌĂǁ ĐŽŶĐůƵƐŝŽŶƐ͘ Ɛ ƐŚŽǁŶ ĨŽƌ ƚŚĞ LRRK2 ĂƐƐŽĐŝĂƟŽŶĂŶĚĞǀĞŶƚŚĞƚŽƚĂůŐĞŶĞͲƐĞƚĂƐƐŽĐŝĂƟŽŶ͕ŝƚŝƐĚƌŝǀĞŶďǇŽŶůǇϭǀĂƌŝĂŶƚ͕

which also could have been detected with the performance of a simple single-marker ĂƐƐŽĐŝĂƟŽŶƚĞƐƚ͘ĞƐŝĚĞƐƚŚĞƉĂƚŚŽŐĞŶŝĐĂƐƐŽĐŝĂƟŽŶƐŝŐŶĂůŽĨƌĂƌĞǀĂƌŝĂŶƚƉ͘'ϮϬϭϵ^͕ǁĞ ŽďƐĞƌǀĞĚĂƐŝŐŶŝĮĐĂŶƚƉƌŽƚĞĐƟǀĞĞīĞĐƚŽĨĂƉƌĞǀŝŽƵƐůǇƉƵďůŝƐŚĞĚĐŽŵŵŽŶŚĂƉůŽƚǇƉĞ͘39 dŚŝƐ ŽďƐĞƌǀĂƟŽŶ ƐƵƉƉŽƌƚƐ ƚŚĞ ƚŚĞŽƌǇ ƚŚĂƚ ŽƚŚĞƌ ǀĂƌŝĂŶƚƐ ǁŝƚŚ ŽƉƉŽƐŝƚĞ ĞīĞĐƚƐ ĐŽƵůĚ ŝŶƚĞƌĂĐƚ ĂŶĚ ƉŽƚĞŶƟĂůůǇ ŝŶŇƵĞŶĐĞ ƚŚĞ ƉĞŶĞƚƌĂŶĐĞ ŽĨ ƉĂƚŚŽŐĞŶŝĐ LRRK2 variants, such ĂƐƉ͘'ϮϬϭϵ^͘ĞƐŝĚĞƐLRRK2, we furthermore detected a NeuroX-based burden of rare CADD variants for SPATA19 that increases PD risk (p = 0.017). Although the biological ĨƵŶĐƟŽŶŽĨSPATA19 ŝƐƉŽŽƌůǇƐƚƵĚŝĞĚ͕ƚŚĞ'dǆƉŽƌƚĂůĚŝƐƉůĂǇƐƐƉĞĐŝĮĐŚŝŐŚĞǆƉƌĞƐƐŝŽŶ ĨŽƌ ƚŚĞ ƚĞƐƟƐ͕ ĚŝŵŝŶŝƐŚŝŶŐ ƚŚĞ ůŝŬĞůŝŚŽŽĚ ƚŚĂƚ ĚĞĨĞĐƚƐ ŽĨ ƚŚŝƐ ŐĞŶĞ ǁŽƵůĚ ĐŽŶƚƌŝďƵƚĞ ƚŽ ŶĞƵƌŽĚĞŐĞŶĞƌĂƟŽŶ͘ ǇƐĞůĞĐƟŶŐŐĞŶĞƐďĂƐĞĚŽŶďŝŽůŽŐŝĐĂůƐŝŵŝůĂƌŝƟĞƐǁĞĂŝŵĞĚƚŽŝĚĞŶƟĨǇƚŚĞƚƌƵĞ ĐĂƵƐĂůůŽĐŝ͘ƐǁĞĞǆƉĞĐƚƚŚĂƚŽŶůǇŽŶĞŐĞŶĞƉĞƌůŽĐƵƐŝƐƚŚĞƚƌƵĞĐĂƵƐĂůŐĞŶĞ͕ǁĞĚŝĚ ŶŽƚĚĞĮŶĞĂŐĞŶĞͲƐĞƚŝŶĐůƵĚŝŶŐĂůůƚŚĞŐĞŶĞƐƵŶĚĞƌŶĞĂƚŚƚŚĞ't^ůŽĐŝĂƐƐƵŵŝŶŐƚŚĞ ŽǀĞƌƌĞƉƌĞƐĞŶƚĂƟŽŶŽĨŶŽŶͲĐĂƵƐĂů ŐĞŶĞƐǁŽƵůĚ ĚŝůƵƚĞĂƉƵƚĂƟǀĞĂƐƐŽĐŝĂƟŽŶƐŝŐŶĂů͘ tĞ ĂĐŬŶŽǁůĞĚŐĞƚŚĂƚƚŚĞƵůƟŵĂƚĞƐƚƌĂƚĞŐǇƚŽƚĞƐƚƚŚĞĞīĞĐƚŽĨƌĂƌĞǀĂƌŝĂŶƚƐŝŶƚŚĞWůŽĐŝ ǁŽƵůĚďĞƚŽƐĞƋƵĞŶĐĞĂůůŐĞŶĞƐŝŶĂůĂƌŐĞĐŽŚŽƌƚ͕ĂŶĚƚĞƐƚƚŚĞĞīĞĐƚŽĨƌĂƌĞǀĂƌŝĂŶƚƐŝŶ ĞĂĐŚŐĞŶĞŝŶĚŝǀŝĚƵĂůůǇ͘&ƵƌƚŚĞƌŵŽƌĞ͕ƐĞƋƵĞŶĐŝŶŐƌĂƚŚĞƌƚŚĂŶŐĞŶŽƚǇƉŝŶŐǁŝůůĚĞĮŶĞŶŽǀĞů ƌĂƌĞǀĂƌŝĂŶƚƐĂŶĚĐŽŶƚƌŝďƵƚĞƚŽĐĂƚĂůŽŐƵŝŶŐƚŚĞŝŶŇƵĞŶĐĞŽĨƌĂƌĞǀĂƌŝĂŶƚƐƵŶĚĞƌŶĞĂƚŚƚŚĞ PD risk loci.

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ƚŚĞ/ƚĂůŝĂŶDŝŶŝƐƚƌǇŽĨ,ĞĂůƚŚͬDŝŶŝƐƚƌǇŽĨĚƵĐĂƟŽŶ͕hŶŝǀĞƌƐŝƟĞƐĂŶĚZĞƐĞĂƌĐŚ the Israeli Ministry of Health

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ϭ͘ ƌĂƐ :͕ 'ƵĞƌƌĞŝƌŽ Z͕ ,ĂƌĚǇ :͘ ^ŶĂƉ^ŚŽƚ͗

'ĞŶĞƟĐƐŽĨWĂƌŬŝŶƐŽŶ͛ƐĚŝƐĞĂƐĞ͘CellϮϬϭϱ͖ 160(3): 570-.e1.

Ϯ͘ EĂůůƐ D͕ WĂŶŬƌĂƚǌ E͕ >ŝůů D͕ Ğƚ Ăů͘ >ĂƌŐĞͲ scale meta-analysis of genome-wide ĂƐƐŽĐŝĂƟŽŶĚĂƚĂŝĚĞŶƟĮĞƐƐŝǆŶĞǁƌŝƐŬůŽĐŝ for Parkinson’s disease. EĂƚƵƌĞ ŐĞŶĞƟĐƐ ϮϬϭϰ͖ϰϲ;ϵͿ͗ϵϴϵͲϵϯ͘ ϯ͘WŝŚůƐƚƌŽŵ>͕dŽŌD͘WĂƌŬŝŶƐŽŶ͛ƐĚŝƐĞĂƐĞ͗tŚĂƚ ƌĞŵĂŝŶƐ ŽĨ ƚŚĞ ͞ŵŝƐƐŝŶŐ ŚĞƌŝƚĂďŝůŝƚǇ͍͟ DŽǀĞŵĞŶƚ ĚŝƐŽƌĚĞƌƐ ͗ ŽĸĐŝĂů ũŽƵƌŶĂů ŽĨ ƚŚĞ DŽǀĞŵĞŶƚ ŝƐŽƌĚĞƌ ^ŽĐŝĞƚǇ ϮϬϭϭ͖ 26(11): 1971-3. ϰ͘<ĞůůĞƌD&͕^ĂĂĚD͕ƌĂƐ:͕ĞƚĂů͘hƐŝŶŐŐĞŶŽŵĞͲ ǁŝĚĞ ĐŽŵƉůĞǆ ƚƌĂŝƚ ĂŶĂůǇƐŝƐ ƚŽ ƋƵĂŶƟĨǇ ͚ŵŝƐƐŝŶŐ ŚĞƌŝƚĂďŝůŝƚǇ͛ ŝŶ WĂƌŬŝŶƐŽŶ͛Ɛ disease. ,ƵŵĂŶŵŽůĞĐƵůĂƌŐĞŶĞƟĐƐϮϬϭϮ͖ 21(22): 4996-5009.

5. Do CB, Tung JY, Dorfman E, et al. Web-based ŐĞŶŽŵĞͲǁŝĚĞ ĂƐƐŽĐŝĂƟŽŶ ƐƚƵĚǇ ŝĚĞŶƟĮĞƐ ƚǁŽ ŶŽǀĞů ůŽĐŝ ĂŶĚ Ă ƐƵďƐƚĂŶƟĂů ŐĞŶĞƟĐ component for Parkinson’s disease. PLoS ŐĞŶĞƟĐƐϮϬϭϭ͖ϳ;ϲͿ͗ĞϭϬϬϮϭϰϭ͘

ϲ͘DĂŶŽůŝŽd͕ŽůůŝŶƐ&^͕ŽǆE:͕ĞƚĂů͘&ŝŶĚŝŶŐ ƚŚĞ ŵŝƐƐŝŶŐ ŚĞƌŝƚĂďŝůŝƚǇ ŽĨ ĐŽŵƉůĞǆ diseases. NatureϮϬϬϵ͖ϰϲϭ;ϳϮϲϱͿ͗ϳϰϳͲϱϯ͘ ϳ͘ ƵŬ K͕ ^ĐŚĂīŶĞƌ ^&͕ ^ĂŵŽĐŚĂ <͕ Ğƚ Ăů͘

Searching for missing heritability: ĚĞƐŝŐŶŝŶŐƌĂƌĞǀĂƌŝĂŶƚĂƐƐŽĐŝĂƟŽŶƐƚƵĚŝĞƐ͘ WƌŽĐĞĞĚŝŶŐƐ ŽĨ ƚŚĞ EĂƟŽŶĂů ĐĂĚĞŵǇ ŽĨ ^ĐŝĞŶĐĞƐ ŽĨ ƚŚĞ hŶŝƚĞĚ ^ƚĂƚĞƐ ŽĨ ŵĞƌŝĐĂ ϮϬϭϰ͖ϭϭϭ;ϰͿ͗ϰϱϱͲϲϰ͘ ϴ͘ EĞůƐŽŶ DZ͕ tĞŐŵĂŶŶ ͕ Śŵ D'͕ Ğƚ Ăů͘ ŶĂďƵŶĚĂŶĐĞŽĨƌĂƌĞĨƵŶĐƟŽŶĂů ǀĂƌŝĂŶƚƐ in 202 drug target genes sequenced in 14,002 people. ^ĐŝĞŶĐĞ ;EĞǁ zŽƌŬ͕ EzͿ ϮϬϭϮ͖ϯϯϳ;ϲϬϵϬͿ͗ϭϬϬͲϰ͘ ϵ͘ dĞŶŶĞƐƐĞŶ :͕ ŝŐŚĂŵ t͕ K͛ŽŶŶŽƌ d͕ Ğƚ Ăů͘ǀŽůƵƟŽŶĂŶĚĨƵŶĐƟŽŶĂůŝŵƉĂĐƚŽĨƌĂƌĞ ĐŽĚŝŶŐǀĂƌŝĂƟŽŶĨƌŽŵĚĞĞƉƐĞƋƵĞŶĐŝŶŐŽĨ ŚƵŵĂŶ ĞǆŽŵĞƐ͘ ^ĐŝĞŶĐĞ ;EĞǁ zŽƌŬ͕ EzͿ ϮϬϭϮ͖ϯϯϳ;ϲϬϵϬͿ͗ϲϰͲϵ͘

10. Lander ES. The new genomics: global views of biology. ^ĐŝĞŶĐĞ ;EĞǁ zŽƌŬ͕ EzͿ ϭϵϵϲ͖ 274(5287): 536-9.

ϭϭ͘WƌŝƚĐŚĂƌĚ:<͕ŽǆE:͘dŚĞĂůůĞůŝĐĂƌĐŚŝƚĞĐƚƵƌĞ of human disease genes: common ĚŝƐĞĂƐĞͲĐŽŵŵŽŶǀĂƌŝĂŶƚ͘͘͘ŽƌŶŽƚ͍Human ŵŽůĞĐƵůĂƌŐĞŶĞƟĐƐϮϬϬϮ͖ϭϭ;ϮϬͿ͗ϮϰϭϳͲϮϯ͘ ϭϮ͘ŽƚƐƚĞŝŶ͕ZŝƐĐŚE͘ŝƐĐŽǀĞƌŝŶŐŐĞŶŽƚǇƉĞƐ

underlying human phenotypes: past successes for mendelian disease, future ĂƉƉƌŽĂĐŚĞƐ ĨŽƌ ĐŽŵƉůĞǆ ĚŝƐĞĂƐĞ͘ Nature ŐĞŶĞƟĐƐϮϬϬϯ͖ϯϯ^ƵƉƉů͗ϮϮϴͲϯϳ͘

ϭϯ͘ ^ŚĂƌŵĂ D͕ <ƌƵŐĞƌ Z͕ 'ĂƐƐĞƌ d͘ &ƌŽŵ ŐĞŶŽŵĞͲǁŝĚĞĂƐƐŽĐŝĂƟŽŶƐƚƵĚŝĞƐƚŽŶĞǆƚͲ ŐĞŶĞƌĂƟŽŶ ƐĞƋƵĞŶĐŝŶŐ͗ ůĞƐƐŽŶƐ ĨƌŽŵ ƚŚĞ past and planning for the future. JAMA neurologyϮϬϭϰ͖ϳϭ;ϭͿ͗ϱͲϲ͘

ϭϰ͘ <ŝĞǌƵŶ ͕ 'ĂƌŝŵĞůůĂ <͕ Ž Z͕ Ğƚ Ăů͘ ǆŽŵĞ ƐĞƋƵĞŶĐŝŶŐ ĂŶĚ ƚŚĞ ŐĞŶĞƟĐ ďĂƐŝƐ ŽĨ ĐŽŵƉůĞǆ ƚƌĂŝƚƐ͘ EĂƚƵƌĞ ŐĞŶĞƟĐƐ ϮϬϭϮ͖ 44(6): 623-30.

15. Bamshad MJ, Ng SB, Bigham AW, et al. ǆŽŵĞƐĞƋƵĞŶĐŝŶŐĂƐĂƚŽŽůĨŽƌDĞŶĚĞůŝĂŶ disease gene discovery. Nature reviews 'ĞŶĞƟĐƐϮϬϭϭ͖ϭϮ;ϭϭͿ͗ϳϰϱͲϱϱ͘

ϭϲ͘ WƵƌĐĞůů ^D͕ DŽƌĂŶ :>͕ &ƌŽŵĞƌ D͕ Ğƚ Ăů͘ ƉŽůǇŐĞŶŝĐ ďƵƌĚĞŶ ŽĨ ƌĂƌĞ ĚŝƐƌƵƉƟǀĞ ŵƵƚĂƟŽŶƐŝŶƐĐŚŝǌŽƉŚƌĞŶŝĂ͘NatureϮϬϭϰ͖ 506(7487): 185-90.

17. Cirulli ET, Lasseigne BN, Petrovski S, et Ăů͘ ǆŽŵĞ ƐĞƋƵĞŶĐŝŶŐ ŝŶ ĂŵǇŽƚƌŽƉŚŝĐ ůĂƚĞƌĂů ƐĐůĞƌŽƐŝƐ ŝĚĞŶƟĮĞƐ ƌŝƐŬ ŐĞŶĞƐ ĂŶĚ pathways. ^ĐŝĞŶĐĞ ;EĞǁ zŽƌŬ͕ EzͿ ϮϬϭϱ͖ 347(6229): 1436-41.

18. Polymeropoulos MH, Lavedan C, Leroy E, et Ăů͘ DƵƚĂƟŽŶ ŝŶ ƚŚĞ ĂůƉŚĂͲƐǇŶƵĐůĞŝŶ ŐĞŶĞ ŝĚĞŶƟĮĞĚ ŝŶ ĨĂŵŝůŝĞƐ ǁŝƚŚ WĂƌŬŝŶƐŽŶ͛Ɛ disease. ^ĐŝĞŶĐĞ ;EĞǁ zŽƌŬ͕ EzͿ ϭϵϵϳ͖ 276(5321): 2045-7.

ϭϵ͘WĂŝƐĂŶͲZƵŝǌ͕:ĂŝŶ^͕ǀĂŶƐt͕ĞƚĂů͘ůŽŶŝŶŐ

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ŽĨ ƚŚĞ ŐĞŶĞ ĐŽŶƚĂŝŶŝŶŐ ŵƵƚĂƟŽŶƐ ƚŚĂƚ ĐĂƵƐĞ WZ<ϴͲůŝŶŬĞĚ WĂƌŬŝŶƐŽŶ͛Ɛ ĚŝƐĞĂƐĞ͘ NeuronϮϬϬϰ͖ϰϰ;ϰͿ͗ϱϵϱͲϲϬϬ͘ ϮϬ͘ ŝŵƉƌŝĐŚ ͕ ŝƐŬƵƉ ^͕ >ĞŝƚŶĞƌ W͕ Ğƚ Ăů͘ DƵƚĂƟŽŶƐ ŝŶ >ZZ<Ϯ ĐĂƵƐĞ ĂƵƚŽƐŽŵĂůͲ dominant parkinsonism with pleomorphic pathology. NeuronϮϬϬϰ͖ϰϰ;ϰͿ͗ϲϬϭͲϳ͘ Ϯϭ͘^ŝŵŽŶͲ^ĂŶĐŚĞǌ:͕^ĐŚƵůƚĞ͕ƌĂƐ:D͕ĞƚĂů͘ 'ĞŶŽŵĞͲǁŝĚĞ ĂƐƐŽĐŝĂƟŽŶ ƐƚƵĚǇ ƌĞǀĞĂůƐ ŐĞŶĞƟĐƌŝƐŬƵŶĚĞƌůǇŝŶŐWĂƌŬŝŶƐŽŶ͛ƐĚŝƐĞĂƐĞ͘ EĂƚƵƌĞŐĞŶĞƟĐƐϮϬϬϵ͖ϰϭ;ϭϮͿ͗ϭϯϬϴͲϭϮ͘ ϮϮ͘ ĚǁĂƌĚƐ d>͕ ^ĐŽƩ t<͕ ůŵŽŶƚĞ ͕ Ğƚ Ăů͘ 'ĞŶŽŵĞͲǁŝĚĞ ĂƐƐŽĐŝĂƟŽŶ ƐƚƵĚǇ ĐŽŶĮƌŵƐ SNPs in SNCA and the MAPT region as common risk factors for Parkinson disease. ŶŶĂůƐŽĨŚƵŵĂŶŐĞŶĞƟĐƐϮϬϭϬ͖ϳϰ;ϮͿ͗ϵϳͲ 109.

Ϯϯ͘ EĂůůƐ D͕ WůĂŐŶŽů s͕ ,ĞƌŶĂŶĚĞǌ '͕ Ğƚ Ăů͘ /ŵƉƵƚĂƟŽŶ ŽĨ ƐĞƋƵĞŶĐĞ ǀĂƌŝĂŶƚƐ ĨŽƌ ŝĚĞŶƟĮĐĂƟŽŶ ŽĨ ŐĞŶĞƟĐ ƌŝƐŬƐ ĨŽƌ Parkinson’s disease: a meta-analysis of ŐĞŶŽŵĞͲǁŝĚĞ ĂƐƐŽĐŝĂƟŽŶ ƐƚƵĚŝĞƐ͘ Lancet ϮϬϭϭ͖ϯϳϳ;ϵϳϲϲͿ͗ϲϰϭͲϵ͘ Ϯϰ͘'ŽŬĞƌͲůƉĂŶK͕^ĐŚŝīŵĂŶŶZ͕>ĂDĂƌĐĂD͕ EƵƐƐďĂƵŵZ>͕DĐ/ŶĞƌŶĞǇͲ>ĞŽ͕^ŝĚƌĂŶƐŬǇ ͘ WĂƌŬŝŶƐŽŶŝƐŵ ĂŵŽŶŐ 'ĂƵĐŚĞƌ ĚŝƐĞĂƐĞ carriers. :ŽƵƌŶĂůŽĨŵĞĚŝĐĂůŐĞŶĞƟĐƐϮϬϬϰ͖ 41(12): 937-40. Ϯϱ͘WĂŶŬƌĂƚǌE͕ĞĞĐŚĂŵ't͕Ğ^ƚĞĨĂŶŽ>͕Ğƚ al. Meta-analysis of Parkinson’s disease: ŝĚĞŶƟĮĐĂƟŽŶŽĨĂŶŽǀĞůůŽĐƵƐ͕Z/dϮ͘Annals of neurologyϮϬϭϮ͖ϳϭ;ϯͿ͗ϯϳϬͲϴϰ͘

Ϯϲ͘ ,ƵŐŚĞƐ :͕ ĂŶŝĞů ^͕ <ŝůĨŽƌĚ >͕ >ĞĞƐ :͘ Accuracy of clinical diagnosis of idiopathic Parkinson’s disease: a clinico-pathological study of 100 cases. Journal of neurology, ŶĞƵƌŽƐƵƌŐĞƌǇ͕ĂŶĚƉƐǇĐŚŝĂƚƌǇϭϵϵϮ͖ϱϱ;ϯͿ͗ 181-4.

Ϯϳ͘,ŽĨŵĂŶ͕ƌƵƐƐĞůůĞ''͕ĂƌǁŝƐŚDƵƌĂĚ^͕Ğƚ Ăů͘dŚĞZŽƩĞƌĚĂŵ^ƚƵĚǇ͗ϮϬϭϲŽďũĞĐƟǀĞƐ and design update. ƵƌŽƉĞĂŶ ũŽƵƌŶĂů ŽĨ ĞƉŝĚĞŵŝŽůŽŐǇϮϬϭϱ͖ϯϬ;ϴͿ͗ϲϲϭͲϳϬϴ͘ Ϯϴ͘ >ŝ ,͕ ƵƌďŝŶ Z͘ &ĂƐƚ ĂŶĚ ĂĐĐƵƌĂƚĞ ƐŚŽƌƚ

read alignment with Burrows-Wheeler transform. ŝŽŝŶĨŽƌŵĂƟĐƐ ;KǆĨŽƌĚ͕ ŶŐůĂŶĚͿϮϬϬϵ͖Ϯϱ;ϭϰͿ͗ϭϳϱϰͲϲϬ͘

Ϯϵ͘ DĐ<ĞŶŶĂ ͕ ,ĂŶŶĂ D͕ ĂŶŬƐ ͕ Ğƚ Ăů͘ dŚĞ 'ĞŶŽŵĞ ŶĂůǇƐŝƐ dŽŽůŬŝƚ͗ Ă DĂƉZĞĚƵĐĞ ĨƌĂŵĞǁŽƌŬ ĨŽƌ ĂŶĂůǇǌŝŶŐ ŶĞǆƚͲŐĞŶĞƌĂƟŽŶ DNA sequencing data. Genome research ϮϬϭϬ͖ϮϬ;ϵͿ͗ϭϮϵϳͲϯϬϯ͘

ϯϬ͘EĂůůƐD͕ƌĂƐ:͕,ĞƌŶĂŶĚĞǌ'͕ĞƚĂů͘EĞƵƌŽy͕ Ă ĨĂƐƚ ĂŶĚ ĞĸĐŝĞŶƚ ŐĞŶŽƚǇƉŝŶŐ ƉůĂƞŽƌŵ ĨŽƌ ŝŶǀĞƐƟŐĂƟŽŶ ŽĨ ŶĞƵƌŽĚĞŐĞŶĞƌĂƟǀĞ diseases. Neurobiology of aging 2014. ϯϭ͘ >ŝůů D͕ ZŽĞŚƌ :d͕ DĐYƵĞĞŶ D͕ Ğƚ Ăů͘

Comprehensive research synopsis and ƐǇƐƚĞŵĂƟĐ ŵĞƚĂͲĂŶĂůǇƐĞƐ ŝŶ WĂƌŬŝŶƐŽŶ͛Ɛ ĚŝƐĞĂƐĞ ŐĞŶĞƟĐƐ͗ dŚĞ W'ĞŶĞ ĚĂƚĂďĂƐĞ͘ W>Ž^ŐĞŶĞƟĐƐϮϬϭϮ͖ϴ;ϯͿ͗ĞϭϬϬϮϱϰϴ͘ ϯϮ͘ tĂŶŐ <͕ >ŝ D͕ ,ĂŬŽŶĂƌƐŽŶ ,͘ EEKsZ͗

ĨƵŶĐƟŽŶĂů ĂŶŶŽƚĂƟŽŶ ŽĨ ŐĞŶĞƟĐ ǀĂƌŝĂŶƚƐ from high-throughput sequencing data. EƵĐůĞŝĐĂĐŝĚƐƌĞƐĞĂƌĐŚϮϬϭϬ͖ϯϴ;ϭϲͿ͗Ğϭϲϰ͘ ϯϯ͘ ŵĞŶĚŽůĂ >D͕ ŽƌƐĐŚŶĞƌ DK͕ ZŽďĞƌƚƐŽŶ W͕ Ğƚ Ăů͘ ĐƟŽŶĂďůĞ ĞǆŽŵŝĐ ŝŶĐŝĚĞŶƚĂů ĮŶĚŝŶŐƐ ŝŶ ϲϱϬϯ ƉĂƌƟĐŝƉĂŶƚƐ͗ ĐŚĂůůĞŶŐĞƐ ŽĨǀĂƌŝĂŶƚĐůĂƐƐŝĮĐĂƟŽŶ͘Genome research ϮϬϭϱ͖Ϯϱ;ϯͿ͗ϯϬϱͲϭϱ͘ ϯϰ͘ <ŝƌĐŚĞƌ D͕ tŝƩĞŶ D͕ :ĂŝŶ W͕ K͛ZŽĂŬ :͕ ŽŽƉĞƌ 'D͘ ŐĞŶĞƌĂů ĨƌĂŵĞǁŽƌŬ ĨŽƌ ĞƐƟŵĂƟŶŐ ƚŚĞ ƌĞůĂƟǀĞ ƉĂƚŚŽŐĞŶŝĐŝƚǇ ŽĨ ŚƵŵĂŶŐĞŶĞƟĐǀĂƌŝĂŶƚƐ͘ϮϬϭϰ͖ϰϲ;ϯͿ͗ϯϭϬͲ 5.

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ĂŶĚ ƉŽƉƵůĂƟŽŶͲďĂƐĞĚ ůŝŶŬĂŐĞ ĂŶĂůǇƐĞƐ͘

ŵĞƌŝĐĂŶũŽƵƌŶĂůŽĨŚƵŵĂŶŐĞŶĞƟĐƐϮϬϬϳ͖ 81(3): 559-75.

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3 ^hWW>DEd>d

dĂďůĞϭ͘WES capture protocols

cases ĐŽŶƚƌŽůƐ /W' /W' RSX1 Nimblegenv2 252 37 1201 Truseq 912 446 0 DŝǆĞĚ 3 1 0 Total 1167 484 1201 DŝǆĞĚсƐĂŵƉůĞƐƚŚĂƚŚĂǀĞďĞĞŶĐĂƉƚƵƌĞĚƵƐŝŶŐƚŚĞϮĚŝƐƟŶĐƚĐĂƉƚƵƌĞŬŝƚƐ͘ dĂďůĞϮ͘ǆĐůƵƐŝŽŶŽĨĞǆŽŶƐďĂƐĞĚŽŶĐĂƉƚƵƌĞŝŶĐŽŶƐŝƐƚĞŶĐŝĞƐ͘

gene exon Source

PD meta ASH1L 21 Truseq

DLG2 1+2 Nimblegenv2

TMEM229B 1+2 Nimblegenv2

TMEM175 1 Nimblegenv2

dĂďůĞϯ͘WĂƌĂŵĞƚĞƌƐĨŽƌƉŽǁĞƌĐĂůĐƵůĂƟŽŶƐ͘

Arguments WES NeuroX

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