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Wow. That implies a resistance of > 100MegOhm.
At that voltage, you will have to be very careful on layout & design, since there would be leakage currents through all sorts of paths of currents greater than that.
The Cockcroft-Walton multiplier is a good choice because no single component would need to carry the entire output voltage. Each is exposed only to the supply voltage.
If you use a boost converter to reach, say 200 V...
then you can apply that to a full H-bridge to turn it into AC square waves...
and apply those to a X5 multiplier.
Screenshot:
The load is 10M to bring out some ripple. It suggests 10 nF capacitors ought to be sufficient to supply relatively smooth 1kV to a 100M load.
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