Does the medical expenses deduction use the combined AGI or individual AGI if filing married but filing separately? My wife has low income and significant medical expense

The deduction uses the individual's AGI on the separate tax return. But note that if you both file as married filing separately and your wife uses itemized deductions, you must also use itemized deductions on your own separate tax return. You cannot use the standard deduction. When you both file as married filing separately, you must either both itemize or both take the standard deduction.

Here's the catch.  If you file separate returns you both have to file the same way.  So if your wife files MFS and wants to itemize to see if she can deduct medical expenses YOU also have to itemize on your own MFS return--even if you do not have enough itemized deductions to exceed your own standard deduction.   And if she has a low income, remember that her refund still cannot be more than she had withheld from her paychecks.  

Try doing some math and see what really works out.  It is a lot easier to compare married filing joint to married filing separately if you use desktop software, but you can compare even using online.

It is not easy to compare MFJ to MFS using online TT but you can do it.  Since you only get one return for each account and user ID, you have to use 3 accounts and user ID’s—one for MFJ and two for each of the MFS returns.  Compare, choose, and file—and pay—accordingly.

It is much easier to do this comparison using the desktop version of TT installed from a CD or downloaded to your own computer.  You pay once for the software and you can prepare multiple returns easily, and it has a “what if” feature that allows comparisons.

If you were legally married at the end of 2020 your filing choices are married filing jointly or married filing separately.

Married Filing Jointly is usually better, even if one spouse had little or no income. When you file a joint return, you and your spouse will get the married filing jointly standard deduction of $24,800 (+$1300 for each spouse 65 or older)  You are eligible for more credits including education credits, earned income credit, child and dependent care credit, and a larger income limit to receive the child tax credit.

If you choose to file married filing separately, both spouses have to file the same way—either you both itemize or you both use standard deduction. Your tax rate will be higher than on a joint return. Some of the special rules for filing separately include: you cannot get earned income credit, education credits, adoption credits, or deductions for student loan interest. A higher percent of your Social Security benefits may be taxable. Your limit for SALT (state and local taxes and sales tax) will be only $5000 per spouse. In many cases you will not be able to take the child and dependent care credit. The amount you can contribute to a retirement account will be affected. If you live in a community property state, you will be required to provide additional information regarding your spouse’s income. ( Community property states:  AZ, CA, ID, LA, NV, NM, TX, WA, WI)

If  you are using online TurboTax to prepare your returns, you will need to prepare two separate returns and pay twice.

https://ttlc.intuit.com/questions/1894449-married-filing-jointly-vs-married-filing-separately

https://ttlc.intuit.com/questions/1901162-married-filing-separately-in-community-property-states

https://ttlc.intuit.com/questions/1894449-is-it-better-for-a-married-couple-to-file-jointly-or-separately